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| [[File:Zeolite-ZSM-5-3D-vdW.png|thumb|X-ray crystallography can locate every atom in a [[zeolite]], an [[aluminosilicate]].]]
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| '''X-ray crystallography''' is a tool used for determining the atomic and molecular structure of a [[crystal]], in which the crystalline [[atom]]s cause a beam of [[X-rays]] to [[Diffraction|diffract]] into many specific directions. By measuring the angles and intensities of these diffracted beams, a [[crystallography|crystallographer]] can produce a three-dimensional picture of the density of [[electron]]s within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their [[chemical bond]]s, their [[Entropy|disorder]] and various other information.
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| Since many materials can form crystals—such as [[salt (chemistry)|salts]], [[metal]]s, [[mineral]]s, [[semiconductor]]s, as well as various inorganic, organic and biological molecules—X-ray crystallography has been fundamental in the development of many scientific fields. In its first decades of use, this method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences among various materials, especially minerals and [[alloy]]s. The method also revealed the structure and function of many biological molecules, including [[vitamin]]s, drugs, [[protein]]s and [[nucleic acid]]s such as [[DNA]]. X-ray crystallography is still the chief method for characterizing the atomic structure of new materials and in discerning materials that appear similar by other [[experiment]]s. X-ray [[crystal structure]]s can also account for unusual [[electronics|electronic]] or [[Deformation (engineering)#Elastic deformation|elastic]] properties of a material, shed light on chemical interactions and processes, or serve as the basis for [[drug design|designing pharmaceuticals against diseases]].
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| In an X-ray diffraction measurement, a [[crystal]] is mounted on a [[goniometer]] and gradually rotated while being bombarded with X-rays, producing a [[diffraction pattern]] of regularly spaced spots known as ''reflections''. The two-dimensional images taken at different rotations are converted into a three-dimensional model of the density of electrons within the crystal using the mathematical method of [[Fourier transform]]s, combined with chemical data known for the sample. Poor resolution (fuzziness) or even errors may result if the crystals are too small, or not uniform enough in their internal makeup.
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| X-ray crystallography is related to several other methods for determining atomic structures. Similar diffraction patterns can be produced by scattering electrons or [[neutron]]s, which are likewise interpreted as a [[Fourier transform]]. If single crystals of sufficient size cannot be obtained, various other X-ray methods can be applied to obtain less detailed information; such methods include [[fiber diffraction]], [[powder diffraction]] and [[small-angle X-ray scattering]] (SAXS).
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| If the material under investigation is only available in the form of [[nanocrystalline]] powders or suffers from poor crystallinity, the methods of [[electron crystallography]] can be applied for determining the atomic structure.
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| For all above mentioned X-ray diffraction methods, the scattering is [[elastic scattering|elastic]]; the scattered X-rays have the same [[wavelength]] as the incoming X-ray. By contrast, ''inelastic'' X-ray scattering methods are useful in studying excitations of the sample, rather than the distribution of its atoms.{{citation needed|date=November 2011}}
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| ==History==
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| ===Early scientific history of crystals and X-rays===
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| [[File:Kepler conjecture 1.jpg|thumb|Drawing of square (Figure A, above) and hexagonal (Figure B, below) packing from [[Johannes Kepler|Kepler's]] work, ''Strena seu de Nive Sexangula''.]]
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| Crystals have long been admired for their regularity and symmetry, but they were not investigated scientifically until the 17th century. [[Johannes Kepler]] hypothesized in his work ''Strena seu de Nive Sexangula'' (A New Year's Gift of Hexagonal Snow) (1611) that the hexagonal symmetry of [[snow|snowflake crystals]] was due to a regular packing of spherical water particles.<ref>{{cite book|author=Kepler J|authorlink=Johannes Kepler|year=1611|title=Strena seu de Nive Sexangula|publisher=G. Tampach|location=Frankfurt|url=http://www.thelatinlibrary.com/kepler/strena.html|isbn=3-321-00021-0}}</ref>
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| [[File:Snowflake8.png|thumb|left|As shown by X-ray crystallography, the hexagonal symmetry of snowflakes results from the [[tetrahedron|tetrahedral]] arrangement of [[hydrogen bond]]s about each water molecule. The water molecules are arranged similarly to the [[silicon]] atoms in the [[tridymite]] [[polymorphism (materials science)|polymorph]] of SiO<sub>2</sub>. The resulting crystal structure has hexagonal symmetry when viewed along a principal axis.]]
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| Crystal symmetry was first investigated experimentally by Danish scientist [[Nicolas Steno]] (1669), who showed that the angles between the faces are the same in every exemplar of a particular type of crystal,<ref>{{cite book|author=Steno N|authorlink=Nicolas Steno|year=1669|title=De solido intra solidum naturaliter contento dissertationis prodromus|publisher=Florentiae}}</ref> and by [[René Just Haüy]] (1784), who discovered that every face of a crystal can be described by simple stacking patterns of blocks of the same shape and size. Hence, [[William Hallowes Miller]] in 1839 was able to give each face a unique label of three small integers, the [[Miller index|Miller indices]] which are still used today for identifying crystal faces. Haüy's study led to the correct idea that crystals are a regular three-dimensional array (a [[Bravais lattice]]) of atoms and [[molecule]]s; a single [[unit cell]] is repeated indefinitely along three principal directions that are not necessarily perpendicular. In the 19th century, a complete catalog of the possible symmetries of a crystal was worked out by [[Johann F. C. Hessel|Johan Hessel]],<ref>{{cite book|author=Hessel JFC|year=1831|title=Kristallometrie oder Kristallonomie und Kristallographie|publisher=Leipzig}}</ref> [[Auguste Bravais]],<ref>{{cite journal|author=Bravais A|authorlink=Auguste Bravais|year=1850|title=Mémoire sur les systèmes formés par des points distribués regulièrement sur un plan ou dans l'espace|journal=Journal de l'Ecole Polytechnique|volume=19|page=1}}</ref> [[Evgraf Fedorov]],<ref>{{Cite journal|author=Shafranovskii I I and Belov N V|title=E. S. Fedorov|journal=50 Years of X-Ray Diffraction, ed. Paul Ewald (Springer)|year=1962|isbn=90-277-9029-9|url=http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/fedorov.pdf|pages=351}}</ref> [[Arthur Moritz Schönflies|Arthur Schönflies]]<ref>{{cite book|author=Schönflies A|authorlink=Arthur Moritz Schönflies|year=1891|title=Kristallsysteme und Kristallstruktur|publisher=Leipzig}}</ref> and (belatedly) [[William Barlow (geologist)|William Barlow]]. From the available data and physical reasoning, Barlow proposed several crystal structures in the 1880s that were validated later by X-ray crystallography;<ref>{{cite journal|author=Barlow W|year = 1883|title=Probable nature of the internal symmetry of crystals|journal=Nature|volume=29|page=186|doi=10.1038/029186a0|issue=738|bibcode = 1883Natur..29..186B }} See also {{cite journal|last1=Barlow|first1=William|title=Probable Nature of the Internal Symmetry of Crystals|journal=Nature|volume=29|pages=205|year=1883|doi=10.1038/029205a0|issue=739|bibcode = 1883Natur..29..205B }} {{cite journal|last1=Sohncke|first1=L.|title=Probable Nature of the Internal Symmetry of Crystals|journal=Nature|volume=29|pages=383|year=1884|doi=10.1038/029383a0|issue=747|bibcode = 1884Natur..29..383S }} {{cite journal|last1=Barlow|first1=WM.|title=Probable Nature of the Internal Symmetry of Crystals|journal=Nature|volume=29|pages=404|year=1884|doi=10.1038/029404b0|issue=748|bibcode = 1884Natur..29..404B }}</ref> however, the available data were too scarce in the 1880s to accept his models as conclusive.
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| [[File:3D model hydrogen bonds in water.svg|thumb|X-ray crystallography shows the arrangement of water molecules in ice, revealing the [[hydrogen bond]]s (1) that hold the solid together. Few other methods can determine the structure of matter with such precision (''resolution'').]]
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| X-rays were discovered by [[Wilhelm Conrad Röntgen]] in 1895, just as the studies of crystal symmetry were being concluded. Physicists were initially uncertain of the nature of X-rays, although it was soon suspected (correctly) that they were waves of [[electromagnetic radiation]], in other words, another form of [[light]]. At that time, the wave model of [[light]]—specifically, the [[James Clerk Maxwell|Maxwell]] theory of [[electromagnetic radiation]]—was well accepted among scientists, and experiments by [[Charles Glover Barkla]] showed that X-rays exhibited phenomena associated with electromagnetic waves, including transverse [[Polarization (waves)|polarization]] and [[spectral line]]s akin to those observed in the visible wavelengths. Single-slit experiments in the laboratory of [[Arnold Sommerfeld]] suggested the [[wavelength]] of X-rays was about 1 [[angstrom]]. However, X-rays are composed of [[photon]]s, and thus are not only waves of electromagnetic radiation but also exhibit particle-like properties. The photon concept was introduced by [[Albert Einstein]] in 1905,<ref>{{cite journal|author=Einstein A|authorlink=Albert Einstein|year=1905|title=Über einen die Erzeugung und Verwandlung des Lichtes betreffenden heuristischen Gesichtspunkt (trans. A Heuristic Model of the Creation and Transformation of Light)|journal=[[Annalen der Physik]]|volume=17|page=132|bibcode = 1905AnP...322..132E |doi = 10.1002/andp.19053220607|issue=6 }} {{de icon}}. An [[s:A Heuristic Model of the Creation and Transformation of Light|English translation]] is available from [[Wikisource]].</ref> but it was not broadly accepted until 1922,<ref>{{cite journal|author=Einstein A|year=1909|title=Über die Entwicklung unserer Anschauungen über das Wesen und die Konstitution der Strahlung (trans. The Development of Our Views on the Composition and Essence of Radiation)|journal=Physikalische Zeitschrift|volume=10|page=817}} {{de icon}}. An [[s:The Development of Our Views on the Composition and Essence of Radiation|English translation]] is available from [[Wikisource]].</ref><ref>{{cite book|author=Pais A|authorlink=Abraham Pais|year=1982|title=Subtle is the Lord: The Science and the Life of Albert Einstein|publisher=[[Oxford University Press]]|isbn=0-19-853907-X}}</ref> when [[Arthur Compton]] confirmed it by the scattering of X-rays from electrons.<ref>{{cite journal|author=Compton A|authorlink=Arthur Compton|year=1923|title=A Quantum Theory of the Scattering of X-rays by Light Elements|url= http://www.aip.org/history/gap/Compton/01_Compton.html|journal=Phys. Rev.|volume=21|page=483|doi=10.1103/PhysRev.21.483|issue=5|bibcode = 1923PhRv...21..483C }}</ref> Therefore, these particle-like properties of X-rays, such as their ionization of gases, caused [[William Henry Bragg]] to argue in 1907 that X-rays were ''not'' electromagnetic radiation.<ref>{{cite journal|author=Bragg WH|authorlink=William Henry Bragg|year = 1907|title=The nature of Röntgen rays|journal=Transactions of the Royal Society of Science of Australia|volume=31|page=94}}</ref><ref>{{cite journal|author=Bragg WH|year = 1908|title=The nature of γ- and X-rays|journal=Nature|volume=77|page=270|doi=10.1038/077270a0|issue=1995|bibcode = 1908Natur..77..270B }} See also {{cite journal|last1=Bragg|first1=W. H.|title=The Nature of the γ and X-Rays|journal=Nature|volume=78|pages=271|year=1908|doi=10.1038/078271a0|issue=2021|bibcode = 1908Natur..78..271B }} {{cite journal|last1=Bragg|first1=W. H.|title=The Nature of the γ and X-Rays|journal=Nature|volume=78|pages=293|year=1908|doi=10.1038/078293d0|issue=2022|bibcode = 1908Natur..78..293B }} {{cite journal|last1=Bragg|first1=W. H.|title=The Nature of X-Rays|journal=Nature|volume=78|pages=665|year=1908|doi=10.1038/078665b0|issue=2035|bibcode = 1908Natur..78R.665B }}</ref><ref>{{cite journal|author=Bragg WH|year = 1910|title=The consequences of the corpuscular hypothesis of the γ- and X-rays, and the range of β-rays|journal=Phil. Mag.|volume=20|page=385|doi=10.1080/14786441008636917|issue=117}}</ref><ref>{{cite journal|author=Bragg WH|year = 1912|title=On the direct or indirect nature of the ionization by X-rays|doi=10.1080/14786440408637253 |journal=Phil. Mag.|volume=23|page=647|issue=136}}</ref> Nevertheless, Bragg's view was not broadly accepted and the observation of [[X-ray diffraction]] in 1912<ref name=L1912 /> confirmed for most scientists that X-rays were a form of electromagnetic radiation.
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| ===X-ray analysis of crystals===
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| [[File:Bragg diffraction 2.svg|thumb|left|The incoming beam (coming from upper left) causes each scatterer to re-radiate a small portion of its intensity as a spherical wave. If scatterers are arranged symmetrically with a separation ''d'', these spherical waves will be in sync (add constructively) only in directions where their path-length difference 2''d'' sin θ equals an integer multiple of the [[wavelength]] λ. In that case, part of the incoming beam is deflected by an angle 2θ, producing a ''reflection'' spot in the [[diffraction pattern]].]]
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| Crystals are regular arrays of atoms, and X-rays can be considered waves of electromagnetic radiation. Atoms scatter X-ray waves, primarily through the atoms' electrons. Just as an ocean wave striking a lighthouse produces secondary circular waves emanating from the lighthouse, so an X-ray striking an electron produces secondary spherical waves emanating from the electron. This phenomenon is known as [[elastic scattering]], and the electron (or lighthouse) is known as the ''scatterer''. A regular array of scatterers produces a regular array of spherical waves. Although these waves cancel one another out in most directions through [[destructive interference]], they add constructively in a few specific directions, determined by [[Bragg's law]]:
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| :<math>2d \sin \theta = n \lambda</math>
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| Here ''d'' is the spacing between diffracting planes, <math>\theta</math> is the incident angle, ''n'' is any integer, and λ is the wavelength of the beam. These specific directions appear as spots on the [[diffraction pattern]] called ''reflections''. Thus, [[X-ray diffraction]] results from an electromagnetic wave (the X-ray) impinging on a regular array of scatterers (the repeating arrangement of atoms within the crystal).
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| X-rays are used to produce the diffraction pattern because their wavelength λ is typically the same order of magnitude (1–100 angstroms) as the spacing ''d'' between planes in the crystal. In principle, any wave impinging on a regular array of scatterers produces [[diffraction]], as predicted first by [[Francesco Maria Grimaldi]] in 1665. To produce significant diffraction, the spacing between the scatterers and the wavelength of the impinging wave should be similar in size. For illustration, the diffraction of sunlight through a bird's feather was first reported by [[James Gregory (astronomer and mathematician)|James Gregory]] in the later 17th century. The first artificial [[diffraction grating]]s for visible light were constructed by [[David Rittenhouse]] in 1787, and [[Joseph von Fraunhofer]] in 1821. However, visible light has too long a wavelength (typically, 5500 angstroms) to observe diffraction from crystals. Prior to the first X-ray diffraction experiments, the spacings between lattice planes in a crystal were not known with certainty.
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| The idea that crystals could be used as a [[diffraction grating]] for [[X-ray]]s arose in 1912 in a conversation between [[Paul Peter Ewald]] and [[Max von Laue]] in the [[Englischer Garten|English Garden]] in [[Munich]]. Ewald had proposed a resonator model of crystals for his thesis, but this model could not be validated using [[visible light]], since the wavelength was much larger than the spacing between the resonators. Von Laue realized that electromagnetic radiation of a shorter wavelength was needed to observe such small spacings, and suggested that X-rays might have a wavelength comparable to the unit-cell spacing in crystals. Von Laue worked with two technicians, Walter Friedrich and his assistant Paul Knipping, to shine a beam of X-rays through a [[Copper(II) sulfate|copper sulfate]] crystal and record its diffraction on a [[photographic plate]]. After being developed, the plate showed a large number of well-defined spots arranged in a pattern of intersecting circles around the spot produced by the central beam.<ref name=L1912 >{{cite journal|author=Friedrich W, Knipping P, von Laue M|year=1912|title=Interferenz-Erscheinungen bei Röntgenstrahlen|journal=Sitzungsberichte der Mathematisch-Physikalischen Classe der Königlich-Bayerischen Akademie der Wissenschaften zu München|volume=1912|page=303}}</ref><ref>{{cite journal|title=Concerning the detection of x-ray interferences|journal=Nobel Lectures, Physics|year=1914|author=von Laue M|volume=1901–1921|url=http://nobelprize.org/nobel_prizes/physics/laureates/1914/laue-lecture.pdf|format=PDF|accessdate=2009-02-18}}</ref> Von Laue developed a law that connects the scattering angles and the size and orientation of the unit-cell spacings in the crystal, for which he was awarded the [[Nobel Prize in Physics]] in 1914.<ref>{{cite book|author=Dana ES, Ford WE|year=1932|title=A Textbook of Mineralogy, fourth edition|location=New York|publisher=John Wiley & Sons|page=28}}</ref> | |
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| ===Scattering===
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| As described in the [[#Diffraction theory|mathematical derivation below]], the X-ray scattering is determined by the density of electrons within the crystal. Since the energy of an X-ray is much greater than that of a valence electron, the scattering may be modeled as [[Thomson scattering]], the interaction of an electromagnetic ray with a free electron. This model is generally adopted to describe the polarization of the scattered radiation.
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| The intensity of Thomson scattering for one particle with mass m is:<ref>{{cite book|author=Andre Guinier|year=1952|title=X-ray Crystallographic Technology|location=London|publisher=Hilger and Watts LTD|page=271}}</ref> | |
| : <math>
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| I_o = I_e \left(\frac{q^4}{m^2c^4}\right)\frac{1+\cos^22\theta}{2} = I_e7.94.10^{-26}\frac{1+\cos^22\theta}{2} = I_ef
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| </math>
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| Hence the atomic nuclei, which are much heavier than an electron, contribute negligibly to the scattered X-rays.
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| ===Development from 1912 to 1920===
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| [[File:Diamond and graphite2.jpg|thumb|Although [[diamond]]s (top left) and [[graphite]] (top right) are identical in chemical composition—being both pure [[carbon]]—X-ray crystallography revealed the arrangement of their atoms (bottom) accounts for their different properties. In diamond, the carbon atoms are arranged [[diamond cubic|tetrahedrally]] and held together by single [[covalent bond]]s, making it strong in all directions. By contrast, graphite is composed of stacked sheets. Within the sheet, the bonding is covalent and has hexagonal symmetry, but there are no covalent bonds between the sheets, making graphite easy to cleave into flakes.]]
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| After Von Laue's pioneering research, the field developed rapidly, most notably by physicists [[William Lawrence Bragg]] and his father [[William Henry Bragg]]. In 1912–1913, the younger Bragg developed [[Bragg's law]], which connects the observed scattering with reflections from evenly spaced planes within the crystal.<ref>{{cite journal|author=Bragg WL|year = 1912|title=The Specular Reflexion of X-rays|journal=Nature|volume=90|page=410|doi=10.1038/090410b0|issue=2250|bibcode = 1912Natur..90..410B }}</ref><ref>{{cite journal|author=Bragg WL|year = 1913|title=The Diffraction of Short Electromagnetic Waves by a Crystal|journal=Proceedings of the Cambridge Philosophical Society|volume=17|page=43}}</ref><ref>{{cite journal|author=Bragg|year = 1914|title=Die Reflexion der Röntgenstrahlen|journal=Jahrbuch der Radioaktivität und Elektronik|volume=11|page=350}}</ref> The Braggs, father and son, shared the 1915 Nobel Prize in Physics for their work in crystallography. The earliest structures were generally simple and marked by one-dimensional symmetry. However, as computational and experimental methods improved over the next decades, it became feasible to deduce reliable atomic positions for more complicated two- and three-dimensional arrangements of atoms in the unit-cell.
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| The potential of X-ray crystallography for determining the structure of molecules and minerals—then only known vaguely from chemical and hydrodynamic experiments—was realized immediately. The earliest structures were simple inorganic crystals and minerals, but even these revealed fundamental laws of physics and chemistry. The first atomic-resolution structure to be "solved" (i.e. determined) in 1914 was that of [[sodium chloride|table salt]].<ref>{{cite journal|author=Bragg|year=1913|title=The Structure of Some Crystals as Indicated by their Diffraction of X-rays|journal=Proc. R. Soc. Lond.|volume=A89|issue=610|jstor=93488|pages=248–277}}</ref><ref>{{cite journal|author=Bragg WL, James RW, Bosanquet CH|year=1921|title=The Intensity of Reflexion of X-rays by Rock-Salt|journal=Phil. Mag.|volume=41|page=309|doi=10.1080/14786442108636225|issue=243}}</ref><ref>{{cite journal|author=Bragg WL, James RW, Bosanquet CH|year=1921|title=The Intensity of Reflexion of X-rays by Rock-Salt. Part II|journal=Phil. Mag.|volume=42|page=1|doi=10.1080/14786442108633730|issue=247 }}</ref> The distribution of electrons in the table-salt structure showed that crystals are not necessarily composed of [[covalent bond|covalently bonded]] molecules, and proved the existence of [[ionic compound]]s.<ref>{{cite journal|author=Bragg WL, James RW, Bosanquet CH|year=1922|title=The Distribution of Electrons around the Nucleus in the Sodium and Chlorine Atoms|journal=Phil. Mag.|volume=44|page=433|doi=10.1080/14786440908565188|issue=261}}</ref> The structure of [[diamond]] was solved in the same year,<ref name=dia >{{cite journal|author=Bragg WH, Bragg WL|year=1913|title=The structure of the diamond|journal=Nature|volume=91|page=557|doi=10.1038/091557a0|issue=2283|bibcode = 1913Natur..91..557B }}</ref><ref>{{cite journal|author=Bragg WH, Bragg WL|year=1913|title=The structure of the diamond|journal= Proc. R. Soc. Lond.|volume=A89|page=277|doi=10.1098/rspa.1913.0084|issue=610|bibcode = 1913RSPSA..89..277B }}</ref> proving the tetrahedral arrangement of its chemical bonds and showing that the length of C–C single bond was 1.52 angstroms. Other early structures included [[copper]],<ref>{{cite journal|author=Bragg WL|year = 1914|title=The Crystalline Structure of Copper|doi=10.1080/14786440908635219 |journal=Phil. Mag.|volume=28|page=355|issue=165}}</ref> [[calcium fluoride]] (CaF<sub>2</sub>, also known as ''fluorite''), [[calcite]] (CaCO<sub>3</sub>) and [[pyrite]] (FeS<sub>2</sub>)<ref name=carb >{{cite journal|author=Bragg WL|year = 1914|title=The analysis of crystals by the X-ray spectrometer|doi=10.1098/rspa.1914.0015 |journal= Proc. R. Soc. Lond.|volume=A89|page=468|issue=613|bibcode = 1914RSPSA..89..468B }}</ref> in 1914; [[spinel]] (MgAl<sub>2</sub>O<sub>4</sub>) in 1915;<ref>{{cite journal|author=Bragg WH|authorlink=William Henry Bragg|year = 1915|title=The structure of the spinel group of crystals|doi=10.1080/14786440808635400 |journal=Phil. Mag.|volume=30|page=305|issue=176}}</ref><ref>{{cite journal|author=Nishikawa S|year = 1915|title=Structure of some crystals of spinel group|journal=Proc. Tokyo Math. Phys. Soc.|volume=8|page=199}}</ref> the [[rutile]] and [[anatase]] forms of [[titanium dioxide]] (TiO<sub>2</sub>) in 1916;<ref>{{cite journal|author=Vegard L|year = 1916|title=Results of Crystal Analysis|doi=10.1080/14786441608635544 |journal=Phil. Mag.|volume=32|page=65|issue=187}}</ref> [[pyrochroite]] Mn(OH)<sub>2</sub> and, by extension, [[brucite]] Mg(OH)<sub>2</sub> in 1919;.<ref>{{cite journal|author=Aminoff G|year = 1919|title=Crystal Structure of Pyrochroite|journal=Stockholm Geol. Fören. Förh.|volume=41|page=407}}</ref><ref>{{cite journal|author=Aminoff G|year = 1921|title=Über die Struktur des Magnesiumhydroxids|journal=Z. Kristallogr.|volume=56|page=505}}</ref> Also in 1919 [[sodium nitrate]] (NaNO<sub>3</sub>) and caesium dichloroiodide (CsICl<sub>2</sub>) were determined by [[Ralph Walter Graystone Wyckoff]], and the [[wurtzite]] (hexagonal ZnS) structure became known in 1920.<ref>{{cite journal|author=Bragg WL|year = 1920|title=The crystalline structure of zinc oxide|doi=10.1080/14786440608636079 |journal=Phil. Mag.|volume=39|page=647|issue=234}}</ref>
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| The structure of [[graphite]] was solved in 1916<ref>{{cite journal|author=[[Peter Debye|Debije P]], Scherrer P|year = 1916|title=Interferenz an regellos orientierten Teilchen im Röntgenlicht I|journal=Physikalische Zeitschrift|volume=17|page=277}}</ref> by the related method of [[powder diffraction]],<ref>{{cite journal|author=Friedrich W|year = 1913|title=Eine neue Interferenzerscheinung bei Röntgenstrahlen|journal=Physikalische Zeitschrift|volume=14|page=317}}</ref> which was developed by [[Peter Debye]] and [[Paul Scherrer]] and, independently, by [[Albert Hull]] in 1917.<ref>{{cite journal|author=Hull AW|authorlink=Albert Hull|year = 1917|title=A New Method of X-ray Crystal Analysis|journal=Phys. Rev.|volume=10|page=661|doi=10.1103/PhysRev.10.661|issue=6|bibcode = 1917PhRv...10..661H }}</ref> The structure of graphite was determined from single-crystal diffraction in 1924 by two groups independently.<ref>{{cite journal|author=Bernal JD|authorlink=John Desmond Bernal|year = 1924|title=The Structure of Graphite|jstor=94336|journal= Proc. R. Soc. Lond.|volume=A106|issue=740|pages=749–773}}</ref><ref>{{cite journal|author=Hassel O, Mack H|year = 1924|title=Über die Kristallstruktur des Graphits|journal=Zeitschrift für Physik|volume=25|page=317|doi=10.1007/BF01327534|bibcode = 1924ZPhy...25..317H }}</ref> Hull also used the powder method to determine the structures of various metals, such as iron<ref>{{cite journal|author=Hull AW|year = 1917|title=The Crystal Structure of Iron|journal=Phys. Rev.|volume=9|page=84}}</ref> and magnesium.<ref>{{cite journal|author=Hull AW|year = 1917|title=The Crystal Structure of Magnesium|journal=PNAS|volume=3|page=470|doi=10.1073/pnas.3.7.470|issue=7|bibcode = 1917PNAS....3..470H }}</ref>
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| ===Cultural and aesthetic importance of X-ray crystallography===
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| In what has been called his scientific autobiography, ''The Development of X-ray Analysis'', Sir [[William Lawrence Bragg]] mentioned that he believed the field of crystallography was particularly welcoming to women because the techno-aesthetics of the molecular structures resembled textiles and household objects. Bragg was known to compare crystal formation to "curtains, wallpapers, mosaics, and roses."<ref>{{cite journal|author=Black, Susan AW|year = 2005|title=Domesticating the Crystal: Sir Lawrence Bragg and the Aesthetics of "X-ray Analysis"|journal=Configurations|volume=13|issue= 2|page=257|}}</ref>
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| In 1951, the Festival Pattern Group at the [[Festival of Britain]] hosted a collaborative group of textile manufacturers and experienced crystallographers to design lace and prints based on the X-ray crystallography of [[insulin]], [[china clay]], and [[hemoglobin]]. One of the leading scientists of the project was Dr. [[Helen Megaw]] (1907–2002), the Assistant Director of Research at the Cavendish Laboratory in Cambridge at the time. Megaw is credited as one of the central figures who took inspiration from crystal diagrams and saw their potential in design.<ref name="WC"/> In 2008, the Wellcome Collection in London curated an exhibition on the Festival Pattern Group called "From Atom to Patterns."<ref name="WC">{{cite web|title=From Atoms To Patterns|url=http://www.wellcomecollection.org/whats-on/exhibitions/from-atoms-to-patterns.aspx|publisher=Wellcome Collection|accessdate=17 October 2013}}</ref>
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| ==Contributions to chemistry and material science==
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| X-ray crystallography has led to a better understanding of [[chemical bond]]s and [[noncovalent bonding|non-covalent interactions]]. The initial studies revealed the typical radii of atoms, and confirmed many theoretical models of chemical bonding, such as the tetrahedral bonding of carbon in the diamond structure,<ref name=dia /> the octahedral bonding of metals observed in ammonium hexachloroplatinate (IV),<ref>{{cite journal|author=Wyckoff RWG, Posnjak E|year = 1921|title=The Crystal Structure of Ammonium Chloroplatinate|journal=J. Amer. Chem. Soc.|volume=43|page=2292|doi=10.1021/ja01444a002|issue=11}}</ref> and the resonance observed in the planar carbonate group<ref name=carb /> and in aromatic molecules.<ref name=antr /> [[Kathleen Lonsdale]]'s 1928 structure of [[hexamethylbenzene]]<ref>{{cite journal|author=Lonsdale K|authorlink=Kathleen Lonsdale|year=1928|title=The structure of the benzene ring|journal=Nature|volume=122|page=810|doi=10.1038/122810c0|issue=3082|bibcode = 1928Natur.122..810L }}</ref> established the hexagonal symmetry of [[benzene]] and showed a clear difference in bond length between the aliphatic C–C bonds and aromatic C–C bonds; this finding led to the idea of [[resonance (chemistry)|resonance]] between chemical bonds, which had profound consequences for the development of chemistry.<ref>{{cite book|author=Pauling L|authorlink=Linus Pauling|title=The Nature of the Chemical Bond|edition = 3rd|publisher=[[Cornell University Press]]|location=Ithaca, NY|isbn=0-8014-0333-2}}</ref> Her conclusions were anticipated by [[William Henry Bragg]], who published models of [[naphthalene]] and [[anthracene]] in 1921 based on other molecules, an early form of [[molecular replacement]].<ref name=antr >{{cite journal|author=Bragg WH|authorlink=William Henry Bragg|year = 1921|title=The structure of organic crystals|doi=10.1088/1478-7814/34/1/306|journal= Proc. R. Soc. Lond.|volume=34|page=33|bibcode = 1921PPSL...34...33B }}</ref><ref>{{cite journal|author=Bragg WH|authorlink=William Henry Bragg|year = 1922|title=The crystalline structure of anthracene|doi=10.1088/1478-7814/35/1/320|journal= Proc. R. Soc. Lond.|volume=35|page=167|bibcode = 1922PPSL...35..167B }}</ref>
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| Also in the 1920s, [[Victor Moritz Goldschmidt]] and later [[Linus Pauling]] developed rules for eliminating chemically unlikely structures and for determining the relative sizes of atoms. These rules led to the structure of [[brookite]] (1928) and an understanding of the relative stability of the [[rutile]], [[brookite]] and [[anatase]] forms of [[titanium dioxide]].
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| The distance between two bonded atoms is a sensitive measure of the bond strength and its [[bond order]]; thus, X-ray crystallographic studies have led to the discovery of even more exotic types of bonding in [[inorganic chemistry]], such as metal-metal double bonds,<ref>{{cite journal|author=Powell HM, Ewens RVG|year=1939|title=The crystal structure of iron enneacarbonyl|journal=J. Chem. Soc.|page=286|doi=10.1039/jr9390000286}}</ref><ref>{{cite journal|author=Bertrand JA, [[F. Albert Cotton|Cotton FA]], Dollase WA|year=1963|title=The Metal-Metal Bonded, Polynuclear Complex Anion in CsReCl<sub>4</sub>|journal=J. Amer. Chem. Soc.|volume=85|page=1349|doi=10.1021/ja00892a029|issue=9}}</ref><ref>{{cite journal|author=Robinson WT, Fergusson JE, Penfold BR|year=1963|title=Configuration of Anion in CsReCl<sub>4</sub>|journal=Proceedings of the Chemical Society of London|page=116}}</ref> metal-metal quadruple bonds,<ref>{{cite journal|author=[[F. Albert Cotton|Cotton FA]], Curtis NF, Harris CB, Johnson BFG, Lippard SJ, Mague JT, Robinson WR, Wood JS|year=1964|title=Mononuclear and Polynuclear Chemistry of Rhenium (III): Its Pronounced Homophilicity|journal=Science|volume=145|doi=10.1126/science.145.3638.1305|pmid = 17802015|issue=3638|bibcode = 1964Sci...145.1305C|pages=1305–7 }}</ref><ref>{{cite journal|author=[[F. Albert Cotton|Cotton FA]], Harris CB|year=1965|title=The Crystal and Molecular Structure of Dipotassium Octachlorodirhenate(III) Dihydrate|journal=Inorganic Chemistry|volume=4|page=330|doi=10.1021/ic50025a015|issue=3}}</ref><ref>{{cite journal|author=Cotton FA|authorlink= F. Albert Cotton|title=Metal-Metal Bonding in [Re<sub>2</sub>X<sub>8</sub>]<sup>2-</sup> Ions and Other Metal Atom Clusters|journal=Inorganic Chemistry|volume=4|page=334|doi=10.1021/ic50025a016|year=1965|issue=3}}</ref> and three-center, two-electron bonds.<ref>{{cite journal|author=Eberhardt WH, Crawford W, Jr., Lipscomb WN|year=1954|title=The valence structure of the boron hydrides|journal=J. Chem. Phys.|volume=22|page=989|doi=10.1063/1.1740320|issue=6}}</ref> X-ray crystallography—or, strictly speaking, an inelastic [[Compton scattering]] experiment—has also provided evidence for the partly covalent character of [[hydrogen bond]]s.<ref>{{cite journal|author=Martin TW, Derewenda ZS|year = 1999|title=The name is Bond—H bond|journal=Nature Structural Biology|volume=6|doi=10.1038/8195|pmid=10331860|issue=5|pages=403–6}}</ref> In the field of [[organometallic chemistry]], the X-ray structure of [[ferrocene]] initiated scientific studies of [[sandwich compounds]],<ref>{{cite journal|author=Dunitz JD, Orgel LE, Rich A|year=1956|title=The crystal structure of ferrocene|journal=Acta Crystallographica|volume=9|page=373|doi=10.1107/S0365110X56001091|issue=4}}</ref><ref>{{cite journal|author=Seiler P, Dunitz JD|year=1979|title=A new interpretation of the disordered crystal structure of ferrocene|doi=10.1107/S0567740879005598 |journal=Acta Crystallographica B|volume=35|page=1068|issue=5}}</ref> while that of [[Zeise's salt]] stimulated research into "back bonding" and metal-pi complexes.<ref>{{cite journal|author=Wunderlich JA, Mellor DP|year=1954|title=A note on the crystal structure of Zeise's salt|journal=Acta Crystallographica|volume=7|page=130|doi=10.1107/S0365110X5400028X}}</ref><ref>{{cite journal|author1=Jarvis JAJ|author2=Kilbourn BT|author3=Owston PG|authorlink3=P. G. Owston|year=1970|title=A re-determination of the crystal and molecular structure of Zeise's salt, KPtCl<sub>3</sub>.C<sub>2</sub>H<sub>4</sub>.H<sub>2</sub>O. A correction|journal=Acta Crystallographica B|volume=26|page=876|doi=10.1107/S056774087000328X|issue=6}}</ref><ref>{{cite journal|author1=Jarvis JAJ|author2=Kilbourn BT|author3=Owston PG|authorlink3=P. G. Owston|year=1971|title=A re-determination of the crystal and molecular structure of Zeise's salt, KPtCl<sub>3</sub>.C<sub>2</sub>H<sub>4</sub>.H<sub>2</sub>O|doi=10.1107/S0567740871002231|journal=Acta Crystallographica B|volume=27|page=366|issue=2}}</ref><ref>{{cite journal|author=Love RA, Koetzle TF, Williams GJB, Andrews LC, Bau R|year=1975|title=Neutron diffraction study of the structure of Zeise's salt, KPtCl<sub>3</sub>(C<sub>2</sub>H<sub>4</sub>).H<sub>2</sub>O|journal=Inorganic Chemistry|volume=14|page=2653|doi=10.1021/ic50153a012|issue=11}}</ref> Finally, X-ray crystallography had a pioneering role in the development of [[supramolecular chemistry]], particularly in clarifying the structures of the [[crown ether]]s and the principles of [[host-guest chemistry]].
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| In material sciences, many complicated [[inorganic]] and [[organometallic]] systems have been analyzed using single-crystal methods, such as [[fullerene]]s, [[porphyrin|metalloporphyrins]], and other complicated compounds. Single-crystal diffraction is also used in the [[pharmaceutical industry]], due to recent problems with [[Polymorphism (materials science)|polymorphs]]. The major factors affecting the quality of single-crystal structures are the crystal's size and regularity; [[Recrystallization (chemistry)|recrystallization]] is a commonly used technique to improve these factors in small-molecule crystals. The [[Cambridge Structural Database]] contains over 500,000 structures; over 99% of these structures were determined by X-ray diffraction.
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| ===Mineralogy and metallurgy===
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| [[File:PIA16217-MarsCuriosityRover-1stXRayView-20121017.jpg|thumb|150px|left|First X-ray diffraction view of [[Martian soil]] - [[CheMin|CheMin analysis]] reveals [[feldspar]], [[pyroxenes]], [[olivine]] and more ([[Curiosity rover]] at "[[Rocknest (Mars)|Rocknest]]", October 17, 2012).<ref name="NASA-20121030" />]]
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| Since the 1920s, X-ray diffraction has been the principal method for determining the arrangement of atoms in minerals and [[metal]]s. The application of X-ray crystallography to [[mineralogy]] began with the structure of [[garnet]], which was determined in 1924 by Menzer. A systematic X-ray crystallographic study of the [[silicate]]s was undertaken in the 1920s. This study showed that, as the [[silicon|Si]]/[[oxygen|O]] ratio is altered, the silicate crystals exhibit significant changes in their atomic arrangements. Machatschki extended these insights to minerals in which [[aluminium]] substitutes for the [[silicon]] atoms of the silicates. The first application of X-ray crystallography to [[metallurgy]] likewise occurred in the mid-1920s.<ref>{{cite journal|author=Westgren A, Phragmén G|year = 1925|title=X-ray Analysis of the Cu-Zn, Ag-Zn and Au-Zn Alloys|journal=Phil. Mag.|volume=50|page=311}}</ref><ref>{{cite journal|author=Bradley AJ, Thewlis J|year = 1926|title=The structure of γ-Brass|journal= Proc. R. Soc. Lond.|volume=112|page=678|doi=10.1098/rspa.1926.0134|issue=762|bibcode = 1926RSPSA.112..678B }}</ref><ref>{{cite journal|author=Hume-Rothery W|year = 1926|title=Researches on the Nature, Properties and Conditions of Formation of Intermetallic Compounds (with special Reference to certain Compounds of Tin)|journal=Journal of the Institute of Metals|volume=35|page=295}}</ref><ref>{{cite journal|author=Bradley AJ, Gregory CH|year = 1927|title=The Structure of certain Ternary Alloys|doi=10.1038/120678a0|journal=Nature|volume=120|page=678|issue=3027|bibcode = 1927Natur.120..678. }}</ref><ref>{{cite journal|author=Westgren A|year = 1932|title=Zur Chemie der Legierungen|journal=Angewandte Chemie|volume=45|page=33|doi=10.1002/ange.19320450202|issue=2}}</ref><ref>{{cite journal|author=Bernal JD|authorlink=John Desmond Bernal|year = 1935|title=The Electron Theory of Metals|journal=Annual Reports on the Progress of Chemistry|volume=32|page=181}}</ref> Most notably, [[Linus Pauling|Linus Pauling's]] structure of the alloy Mg<sub>2</sub>Sn<ref>{{cite journal|author=Pauling L|title=The Crystal Structure of Magnesium Stannide|journal=J. Amer. Chem. Soc.|volume=45|page=2777|doi=10.1021/ja01665a001|year=1923|issue=12}}</ref> led to his theory of the stability and structure of complex ionic crystals.<ref>{{cite journal|author=Pauling L|title=The Principles Determining the Structure of Complex Ionic Crystals|journal=J. Amer. Chem. Soc.|volume=51|page=1010|doi=10.1021/ja01379a006|year=1929|issue=4}}</ref>
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| On October 17, 2012, the [[Curiosity rover]] on the [[Mars|planet Mars]] at "[[Rocknest (Mars)|Rocknest]]" performed the first [[X-ray_crystallography#Mineralogy_and_metallurgy|X-ray diffraction analysis]] of [[Martian soil]]. The results from the rover's [[CheMin|CheMin analyzer]] revealed the presence of several minerals, including [[feldspar]], [[pyroxenes]] and [[olivine]], and suggested that the Martian soil in the sample was similar to the "weathered [[Basalt|basaltic soils]]" of [[Hawaii Volcanoes|Hawaiian volcanoes]].<ref name="NASA-20121030">{{cite web |last=Brown |first=Dwayne |title=NASA Rover's First Soil Studies Help Fingerprint Martian Minerals |url=http://www.nasa.gov/home/hqnews/2012/oct/HQ_12-383_Curiosity_CheMin.html |date=October 30, 2012 |publisher=[[NASA]] |accessdate=October 31, 2012}}</ref>
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| ===Early organic and small biological molecules===
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| [[File:penicillin.png|thumb|The three-dimensional structure of [[penicillin]], solved by [[Dorothy Crowfoot Hodgkin]] in 1945. The green, white, red, yellow and blue spheres represent atoms of [[carbon]], [[hydrogen]], [[oxygen]], [[sulfur]] and [[nitrogen]], respectively.]]
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| The first structure of an organic compound, [[hexamethylenetetramine]], was solved in 1923.<ref>{{cite journal|author=Dickinson RG, Raymond AL|year=1923|title=The Crystal Structure of Hexamethylene-Tetramine|journal=J. Amer. Chem. Soc.|volume=45|page=22|doi=10.1021/ja01654a003}}</ref> This was followed by several studies of long-chain [[fatty acid]]s, which are an important component of biological membranes.<ref>{{cite journal|author=Müller A|year = 1923|title=The X-ray Investigation of Fatty Acids|journal=Journal of the Chemical Society (London)|volume=123|page=2043}}</ref><ref>{{cite journal|author=Saville WB, Shearer G|year = 1925|title=An X-ray Investigation of Saturated Aliphatic Ketones|journal=Journal of the Chemical Society (London)|volume=127|page=591}}</ref><ref>{{cite journal|author=Bragg WH|authorlink=William Henry Bragg|year = 1925|title=The Investigation of thin Films by Means of X-rays|journal=Nature|volume=115|page=266|doi=10.1038/115266a0|issue=2886|bibcode = 1925Natur.115..266B }}</ref><ref>{{cite journal|author=[[Maurice de Broglie|de Broglie M]], Trillat JJ|year = 1925|title=Sur l'interprétation physique des spectres X d'acides gras|journal=Comptes rendus hebdomadaires des séances de l'Académie des sciences|volume=180|page=1485}}</ref><ref>{{cite journal|author=Trillat JJ|year=1926|title=Rayons X et Composeés organiques à longe chaine. Recherches spectrographiques sue leurs structures et leurs orientations|journal=[[Annales de physique]]|volume=6|page=5}}</ref><ref>{{cite journal|author=Caspari WA|year = 1928|title=Crystallography of the Aliphatic Dicarboxylic Acids|journal=Journal of the Chemical Society (London)|volume=?|page=3235}}</ref><ref>{{cite journal|author=Müller A|year = 1928|title=X-ray Investigation of Long Chain Compounds (n. Hydrocarbons)|journal= Proc. R. Soc. Lond.|volume=120|page=437|doi=10.1098/rspa.1928.0158|issue=785|bibcode = 1928RSPSA.120..437M }}</ref><ref>{{cite journal|author=Piper SH|year = 1929|title=Some Examples of Information Obtainable from the long Spacings of Fatty Acids|journal=Transactions of the Faraday Society|volume=25|page=348|doi=10.1039/tf9292500348}}</ref><ref>{{cite journal|author=Müller A|year = 1929|title=The Connection between the Zig-Zag Structure of the Hydrocarbon Chain and the Alternation in the Properties of Odd and Even Numbered Chain Compounds|journal= Proc. R. Soc. Lond.|volume=124|page=317|doi=10.1098/rspa.1929.0117|issue=794|bibcode = 1929RSPSA.124..317M }}</ref> In the 1930s, the structures of much larger molecules with two-dimensional complexity began to be solved. A significant advance was the structure of [[phthalocyanine]],<ref>{{cite journal|author=Robertson JM|year=1936|title=An X-ray Study of the Phthalocyanines, Part II|journal=Journal of the Chemical Society|page=1195}}</ref> a large planar molecule that is closely related to [[porphyrin|porphyrin molecules]] important in biology, such as [[heme]], [[corrin]] and [[chlorophyll]].
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| X-ray crystallography of biological molecules took off with [[Dorothy Crowfoot Hodgkin]], who solved the structures of [[cholesterol]] (1937), [[penicillin]] (1946) and [[vitamin B12]] (1956), for which she was awarded the [[Nobel Prize in Chemistry]] in 1964. In 1969, she succeeded in solving the structure of [[insulin]], on which she worked for over thirty years.<ref>{{cite journal|author=Crowfoot Hodgkin D|authorlink=Dorothy Crowfoot Hodgkin|year = 1935|title=X-ray Single Crystal Photographs of Insulin|journal=Nature|volume=135|page=591|doi=10.1038/135591a0|issue=3415|bibcode = 1935Natur.135..591C }}</ref>
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| [[File:Myoglobin.png|thumb|left|[[Ribbon diagram]] of the structure of [[myoglobin]], showing colored [[alpha helix|alpha helices]]. Such [[protein]]s are long, linear [[molecule]]s with thousands of atoms; yet the relative position of each atom has been determined with sub-atomic resolution by X-ray crystallography. Since it is difficult to visualize all the atoms at once, the ribbon shows the rough path of the protein [[polymer]] from its N-terminus (blue) to its C-terminus (red).]]
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| ===Biological macromolecular crystallography===
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| Crystal structures of proteins (which are irregular and hundreds of times larger than cholesterol) began to be solved in the late 1950s, beginning with the structure of [[sperm whale]] [[myoglobin]] by [[John Kendrew|Sir John Cowdery Kendrew]],<ref>{{Cite journal|doi=10.1038/181662a0|volume=181|issue=4610|author=Kendrew J. C.|authorlink=John Kendrew|title=A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis|journal=Nature|date = 1958-03-08|pmid=13517261|bibcode = 1958Natur.181..662K|author-separator=,|display-authors=1|last2=Bodo|first2=G.|last3=Dintzis|first3=H. M.|last4=Parrish|first4=R. G.|last5=Wyckoff|first5=H.|last6=Phillips|first6=D. C.|pages=662–6 }}</ref> for which he shared the [[Nobel Prize in Chemistry]] with [[Max Perutz]] in 1962. Since that success, over 73761 X-ray crystal structures of proteins, nucleic acids and other biological molecules have been determined.<ref>{{cite web|url=http://www.rcsb.org/pdb/statistics/holdings.do|title=Table of entries in the PDB, arranged by experimental method}}</ref> For comparison, the nearest competing method in terms of structures analyzed is [[Protein nuclear magnetic resonance spectroscopy|nuclear magnetic resonance (NMR) spectroscopy]], which has resolved 9561 chemical structures.<ref>{{cite web|url=http://pdbbeta.rcsb.org/pdb/static.do?p=general_information/pdb_statistics/index.html|title=PDB Statistics|publisher=RCSB Protein Data Bank|accessdate = 2010-02-09}}</ref> Moreover, crystallography can solve structures of arbitrarily large molecules, whereas solution-state NMR is restricted to relatively small ones (less than 70 k[[atomic mass unit|Da]]). X-ray crystallography is now used routinely by scientists to determine how a pharmaceutical drug interacts with its protein target and what changes might improve it.<ref>{{cite journal|author=Scapin G|title=Structural biology and drug discovery|journal=Curr. Pharm. Des.|volume=12|year=2006|pmid=16796557|doi=10.2174/138161206777585201|issue=17|pages=2087–97}}</ref> However, intrinsic membrane proteins remain challenging to crystallize because they require detergents or other means to solubilize them in isolation, and such detergents often interfere with crystallization. Such membrane proteins are a large component of the genome and include many proteins of great physiological importance, such as [[ion channel]]s and [[receptor (biochemistry)|receptors]].<ref>{{cite journal|author=Lundstrom K|title=Structural genomics for membrane proteins|journal=Cell. Mol. Life Sci.|volume=63|year=2006|pmid=17013556|doi=10.1007/s00018-006-6252-y|issue=22|pages=2597–607}}</ref><ref>{{cite journal|author=Lundstrom K|title=Structural genomics on membrane proteins: mini review|journal=Comb. Chem. High Throughput Screen.|volume=7|year=2004|pmid=15320710|issue=5|pages=431–9}}</ref>
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| ==Relationship to other scattering techniques==
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| {{further2|[[X-ray scattering techniques]]}}
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| ===Elastic vs. inelastic scattering===
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| X-ray crystallography is a form of [[elastic scattering]]; the outgoing X-rays have the same energy, and thus same wavelength, as the incoming X-rays, only with altered direction. By contrast, ''inelastic scattering'' occurs when energy is transferred from the incoming X-ray to the crystal, e.g., by exciting an inner-shell electron to a higher [[energy level]]. Such inelastic scattering reduces the energy (or increases the wavelength) of the outgoing beam. Inelastic scattering is useful for probing such excitations of matter, but not in determining the distribution of scatterers within the matter, which is the goal of X-ray crystallography.
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| [[X-ray]]s range in wavelength from 10 to 0.01 [[nanometers]]; a typical wavelength used for crystallography is 1 [[angstrom|Å]] (0.1 nm){{citation needed|date=October 2011}}, which is on the scale of covalent [[chemical bond]]s and the radius of a single atom. Longer-wavelength photons (such as [[ultraviolet]] [[electromagnetic radiation|radiation]]) would not have sufficient resolution to determine the atomic positions. At the other extreme, shorter-wavelength photons such as [[gamma ray]]s are difficult to produce in large numbers, difficult to focus, and interact too strongly with matter, producing [[pair production|particle-antiparticle pairs]]. Therefore, X-rays are the "sweetspot" for wavelength when determining atomic-resolution structures from the scattering of [[electromagnetic radiation]].
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| ===Other X-ray techniques===
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| Other forms of elastic X-ray scattering include [[powder diffraction]], [[SAXS]] and several types of X-ray [[fiber diffraction]], which was used by [[Rosalind Franklin]] in determining the [[double helix|double-helix structure]] of [[DNA]]. In general, single-crystal X-ray diffraction offers more structural information than these other techniques; however, it requires a sufficiently large and regular crystal, which is not always available.
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| These scattering methods generally use ''monochromatic'' X-rays, which are restricted to a single wavelength with minor deviations. A broad spectrum of X-rays (that is, a blend of X-rays with different wavelengths) can also be used to carry out X-ray diffraction, a technique known as the Laue method. This is the method used in the original discovery of X-ray diffraction. Laue scattering provides much structural information with only a short exposure to the X-ray beam, and is therefore used in structural studies of very rapid events ([[Time resolved crystallography]]). However, it is not as well-suited as monochromatic scattering for determining the full atomic structure of a crystal and therefore works better with crystals with relatively simple atomic arrangements.
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| The Laue back reflection mode records X-rays scattered backwards from a broad spectrum source. This is useful if the sample is too thick for X-rays to transmit through it. The diffracting planes in the crystal are determined by knowing that the normal to the diffracting plane bisects the angle between the incident beam and the diffracted beam. A [[Greninger chart]] can be used <ref>{{cite journal|author=Greninger AB|journal=Zeitschrift fur Kristallographie|volume=91|year=1935|page=424}}</ref> to interpret the back reflection Laue photograph.
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| ===Electron and neutron diffraction===
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| Other particles, such as electrons and [[neutron]]s, may be used to produce a [[diffraction pattern]]. Although electron, neutron, and X-ray scattering are based on different physical processes, the resulting diffraction patterns are analyzed using the same [[coherent diffraction imaging]] techniques.
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| As derived below, the electron density within the crystal and the diffraction patterns are related by a simple mathematical method, the [[Fourier transform]], which allows the density to be calculated relatively easily from the patterns. However, this works only if the scattering is ''weak'', i.e., if the scattered beams are much less intense than the incoming beam. Weakly scattered beams pass through the remainder of the crystal without undergoing a second scattering event. Such re-scattered waves are called "secondary scattering" and hinder the analysis. Any sufficiently thick crystal will produce secondary scattering, but since X-rays interact relatively weakly with the electrons, this is generally not a significant concern. By contrast, electron beams may produce strong secondary scattering even for relatively thin crystals (>100 nm). Since this thickness corresponds to the diameter of many [[virus]]es, a promising direction is the electron diffraction of isolated [[macromolecular assemblies]], such as [[virus|viral]] [[capsid]]s and molecular machines, which may be carried out with a cryo-[[electron microscope]]. Moreover the strong interaction of electrons with matter (about 1000 times stronger than for X-rays) allows determination of the atomic structure of extremely small volumes. The field of applications for [[electron crystallography]] ranges from bio molecules like membrane proteins over organic thin films to the complex structures of (nanocrystalline) intermetallic compounds and zeolites.
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| Neutron diffraction is an excellent method for structure determination, although it has been difficult to obtain intense, monochromatic beams of neutrons in sufficient quantities. Traditionally, [[nuclear reactor]]s have been used, although the new [[Spallation Neutron Source]] holds much promise in the near future. Being uncharged, neutrons scatter much more readily from the atomic nuclei rather than from the electrons. Therefore, neutron scattering is very useful for observing the positions of light atoms with few electrons, especially [[hydrogen]], which is essentially invisible in the X-ray diffraction. Neutron scattering also has the remarkable property that the solvent can be made invisible by adjusting the ratio of normal [[water]], H<sub>2</sub>O, and [[heavy water]], D<sub>2</sub>O.
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| ==Synchrotron Radiation==
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| Synchrotron Radiation is one of the brightest lights on earth. It is the single most powerful tool available to X-ray crystallographers. It is made of X-ray beams generated in large machines called synchrotrons. These machines accelerate electrically charged particles, often electrons, to nearly the speed of light, then whip them around a huge, hollow metal ring.
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| Synchrotrons were originally designed for use by high-energy physicists studying subatomic particles and cosmic phenomena. The largest component of each synchrotron is its electron storage ring. This ring is actually not a perfect circle, but a many-sided polygon. At each corner of the polygon, precisely aligned magnets bend the electron stream, forcing it to stay in the ring. Each time the electrons’ path is bent,
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| they emit bursts of energy in the form of electromagnetic radiation. Because particles in a synchrotron are hurtling at nearly the speed of light, they emit intense radiation, including lots of high-energy X-rays.
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| ==Methods==
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| ===Overview of single-crystal X-ray diffraction===
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| [[File:X ray diffraction.png|thumb|Workflow for solving the structure of a molecule by X-ray crystallography.]]
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| The oldest and most precise method of X-ray [[crystallography]] is ''single-crystal X-ray diffraction'', in which a beam of X-rays strikes a single crystal, producing scattered beams. When they land on a piece of film or other detector, these beams make a ''diffraction pattern'' of spots; the strengths and angles of these beams are recorded as the crystal is gradually rotated.<ref>An analogous diffraction pattern may be observed by shining a laser pointer on a [[compact disc]] or [[DVD]]; the periodic spacing of the CD tracks corresponds to the periodic arrangement of atoms in a crystal.</ref> Each spot is called a ''reflection'', since it corresponds to the reflection of the X-rays from one set of evenly spaced planes within the crystal. For single crystals of sufficient purity and regularity, X-ray diffraction data can determine the mean chemical bond lengths and angles to within a few thousandths of an angstrom and to within a few tenths of a [[degree (angle)|degree]], respectively. The atoms in a crystal are not static, but oscillate about their mean positions, usually by less than a few tenths of an angstrom. X-ray crystallography allows measuring the size of these oscillations.
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| ====Procedure====
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| The technique of single-crystal X-ray crystallography has three basic steps. The first—and often most difficult—step is to obtain an adequate crystal of the material under study. The crystal should be sufficiently large (typically larger than 0.1 mm in all dimensions), pure in composition and regular in structure, with no significant internal [[crystal defect|imperfections]] such as cracks or [[crystal twinning|twinning]].
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| In the second step, the crystal is placed in an intense beam of X-rays, usually of a single wavelength (''monochromatic X-rays''), producing the regular pattern of reflections. As the crystal is gradually rotated, previous reflections disappear and new ones appear; the intensity of every spot is recorded at every orientation of the crystal. Multiple data sets may have to be collected, with each set covering slightly more than half a full rotation of the crystal and typically containing tens of thousands of reflections.
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| In the third step, these data are combined computationally with complementary chemical information to produce and refine a model of the arrangement of atoms within the crystal. The final, refined model of the atomic arrangement—now called a ''[[crystal structure]]''—is usually stored in a public database.
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| ====Limitations====
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| {{see also|Resolution (electron density)}}
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| As the crystal's repeating unit, its unit cell, becomes larger and more complex, the atomic-level picture provided by X-ray crystallography becomes less well-resolved (more "fuzzy") for a given number of observed reflections. Two limiting cases of X-ray crystallography—"small-molecule" and "macromolecular" crystallography—are often discerned. ''Small-molecule crystallography'' typically involves crystals with fewer than 100 atoms in their [[crystal structure|asymmetric unit]]; such crystal structures are usually so well resolved that the atoms can be discerned as isolated "blobs" of electron density. By contrast, ''macromolecular crystallography'' often involves tens of thousands of atoms in the unit cell. Such crystal structures are generally less well-resolved (more "smeared out"); the atoms and chemical bonds appear as tubes of electron density, rather than as isolated atoms. In general, small molecules are also easier to crystallize than macromolecules; however, X-ray crystallography has proven possible even for [[virus]]es with hundreds of thousands of atoms.
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| ===Crystallization===
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| {{further2|[[Crystallization]], [[Recrystallization (chemistry)#Single perfect crystals (for X-ray analysis)|Recrystallization]], and [[Protein crystallization]]}}
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| [[File:Protein crystal.jpg|thumb|left|A protein crystal seen under a [[microscope]]. Crystals used in X-ray crystallography may be smaller than a millimeter across.]]
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| Although crystallography can be used to characterize the disorder in an impure or irregular crystal, crystallography generally requires a pure crystal of high regularity to solve the structure of a complicated arrangement of atoms. Pure, regular crystals can sometimes be obtained from natural or synthetic materials, such as samples of [[metal]]s, minerals or other macroscopic materials. The regularity of such crystals can sometimes be improved with macromolecular crystal [[annealing (metallurgy)|annealing]] <ref>{{cite journal|doi=10.1107/S0907444997019008|last1=Harp|first1=JM|last2=Timm|first2=DE|last3=Bunick|first3=GJ|title=Macromolecular crystal annealing: overcoming increased mosaicity associated with cryocrystallography|journal=Acta crystallographica D|volume=54|issue=Pt 4|pages=622–8|year=1998|pmid=9761858}}</ref><ref>{{cite journal|doi=10.1107/S0907444999005442|last1=Harp|first1=JM|last2=Hanson|first2=BL|last3=Timm|first3=DE|last4=Bunick|first4=GJ|title=Macromolecular crystal annealing: evaluation of techniques and variables|journal=Acta Crystallographica D|volume=55|issue=Pt 7|pages=1329–34|year=1999|pmid=10393299}}</ref><ref>{{cite journal|doi=10.1016/S0076-6879(03)68012-2|last1=Hanson|first1=BL|last2=Harp|first2=JM|last3=Bunick|first3=GJ|title=The well-tempered protein crystal: annealing macromolecular crystals|journal=Methods in enzymology|volume=368|pages=217–35|year=2003|pmid=14674276|series=Methods in Enzymology|isbn=978-0-12-182271-2}}</ref> and other methods. However, in many cases, obtaining a diffraction-quality crystal is the chief barrier to solving its atomic-resolution structure.<ref>{{cite journal|author=Geerlof A|title=The impact of protein characterization in structural proteomics|journal=Acta Crystallographica D |volume=62|year=2006|pmid=17001090|doi=10.1107/S0907444906030307|issue=Pt 10|author-separator=,|display-authors=1|last2=Brown|first2=J.|last3=Coutard|first3=B.|last4=Egloff|first4=M.-P.|last5=Enguita|first5=F. J.|last6=Fogg|first6=M. J.|last7=Gilbert|first7=R. J. C.|last8=Groves|first8=M. R.|last9=Haouz|first9=A.|pages=1125–36}}</ref>
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| Small-molecule and macromolecular crystallography differ in the range of possible techniques used to produce diffraction-quality crystals. Small molecules generally have few degrees of conformational freedom, and may be crystallized by a wide range of methods, such as [[chemical vapor deposition]] and [[Recrystallization (chemistry)#Single perfect crystals (for X-ray analysis)|recrystallization]]. By contrast, macromolecules generally have many degrees of freedom and their crystallization must be carried out to maintain a stable structure. For example, proteins and larger [[RNA]] molecules cannot be crystallized if their tertiary structure has been [[Denaturation (biochemistry)|unfolded]]; therefore, the range of crystallization conditions is restricted to solution conditions in which such molecules remain folded.
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| [[File:CrystalDrops.svg|thumb|upright|Three methods of preparing crystals, A: Hanging drop. B: Sitting drop. C: Microdialysis]] Protein crystals are almost always grown in solution. The most common approach is to lower the solubility of its component molecules very gradually; if this is done too quickly, the molecules will precipitate from solution, forming a useless dust or amorphous gel on the bottom of the container. Crystal growth in solution is characterized by two steps: ''nucleation'' of a microscopic crystallite (possibly having only 100 molecules), followed by ''growth'' of that crystallite, ideally to a diffraction-quality crystal.<ref>{{cite journal|author=Chernov AA|title=Protein crystals and their growth|journal=J. Struct. Biol.|volume=142|year=2003|pmid=12718915|doi=10.1016/S1047-8477(03)00034-0|issue=1|pages=3–21}}</ref> The solution conditions that favor the first step (nucleation) are not always the same conditions that favor the second step (subsequent growth). The crystallographer's goal is to identify solution conditions that favor the development of a single, large crystal, since larger crystals offer improved resolution of the molecule. Consequently, the solution conditions should ''disfavor'' the first step (nucleation) but ''favor'' the second (growth), so that only one large crystal forms per droplet. If nucleation is favored too much, a shower of small crystallites will form in the droplet, rather than one large crystal; if favored too little, no crystal will form whatsoever.
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| It is extremely difficult to predict good conditions for nucleation or growth of well-ordered crystals.<ref>{{cite journal|author=Rupp B, Wang J|title=Predictive models for protein crystallization|journal=Methods|volume=34|year=2004|pmid=15325656|doi=10.1016/j.ymeth.2004.03.031|issue=3|pages=390–407}}</ref> In practice, favorable conditions are identified by ''screening''; a very large batch of the molecules is prepared, and a wide variety of crystallization solutions are tested.<ref>{{cite journal|author=Chayen NE|title=Methods for separating nucleation and growth in protein crystallization|journal=Prog. Biophys. Mol. Biol.|volume=88|year=2005|pmid=15652248|doi=10.1016/j.pbiomolbio.2004.07.007|issue=3|pages=329–37}}</ref> Hundreds, even thousands, of solution conditions are generally tried before finding the successful one. The various conditions can use one or more physical mechanisms to lower the solubility of the molecule; for example, some may change the pH, some contain salts of the [[Hofmeister series]] or chemicals that lower the dielectric constant of the solution, and still others contain large polymers such as [[polyethylene glycol]] that drive the molecule out of solution by entropic effects. It is also common to try several temperatures for encouraging crystallization, or to gradually lower the temperature so that the solution becomes supersaturated. These methods require large amounts of the target molecule, as they use high concentration of the molecule(s) to be crystallized. Due to the difficulty in obtaining such large quantities ([[milligrams]]) of crystallization grade protein, robots have been developed that are capable of accurately dispensing crystallization trial drops that are in the order of 100 [[nanoliter]]s in volume. This means that 10-fold less protein is used per-experiment when compared to crystallization trials setup by hand (in the order of 1 [[microliter]]).<ref>{{cite journal|author=Stock D, Perisic O, Lowe J|title=Robotic nanolitre protein crystallisation at the MRC Laboratory of Molecular Biology|journal=Prog Biophys Mol Biol|volume=88|year=2005|pmid=15652247|doi=10.1016/j.pbiomolbio.2004.07.009|issue=3|pages=311–27}}</ref>
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| Several factors are known to inhibit or mar crystallization. The growing crystals are generally held at a constant temperature and protected from shocks or vibrations that might disturb their crystallization. Impurities in the molecules or in the crystallization solutions are often inimical to crystallization. Conformational flexibility in the molecule also tends to make crystallization less likely, due to entropy. Ironically, molecules that tend to self-assemble into regular helices are often unwilling to assemble into crystals. Crystals can be marred by [[Crystal twinning|twinning]], which can occur when a unit cell can pack equally favorably in multiple orientations; although recent advances in computational methods may allow solving the structure of some twinned crystals. Having failed to crystallize a target molecule, a crystallographer may try again with a slightly modified version of the molecule; even small changes in molecular properties can lead to large differences in crystallization behavior.
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| ===Data collection===
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| ====Mounting the crystal====
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| [[File:Kappa goniometer animation.ogg|thumb|left|Animation showing the five motions possible with a four-circle kappa goniometer. The rotations about each of the four angles φ, κ, ω and 2θ leave the crystal within the X-ray beam, but change the crystal orientation. The detector (red box) can be slid closer or further away from the crystal, allowing higher resolution data to be taken (if closer) or better discernment of the Bragg peaks (if further away).]]
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| The crystal is mounted for measurements so that it may be held in the X-ray beam and rotated. There are several methods of mounting. In the past, crystals were loaded into glass capillaries with the crystallization solution (the [[mother liquor]]). Nowadays, crystals of small molecules are a typically attached with oil or glue to a glass fiber or a loop, which is made of nylon or plastic and attached to a solid rod. Protein crystals are scooped up by a loop, then flash-frozen with [[liquid nitrogen]].<ref>{{cite journal|author=Jeruzalmi D|title=First analysis of macromolecular crystals: biochemistry and x-ray diffraction|journal=Methods Mol. Biol.|volume=364|year=2006|pmid=17172760|doi=10.1385/1-59745-266-1:43|isbn=1-59745-266-1|pages=43–62}}</ref> This freezing reduces the radiation damage of the X-rays, as well as the noise in the Bragg peaks due to thermal motion (the Debye-Waller effect). However, untreated protein crystals often crack if flash-frozen; therefore, they are generally pre-soaked in a cryoprotectant solution before freezing.<ref>{{cite journal|author=Helliwell JR|title=Protein crystal perfection and its application|journal=Acta Crystallographica D|volume=61|year=2005|pmid=15930642|doi=10.1107/S0907444905001368|issue=Pt 6|pages=793–8}}</ref> Unfortunately, this pre-soak may itself cause the crystal to crack, ruining it for crystallography. Generally, successful cryo-conditions are identified by trial and error.
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| The capillary or loop is mounted on a [[goniometer]], which allows it to be positioned accurately within the X-ray beam and rotated. Since both the crystal and the beam are often very small, the crystal must be centered within the beam to within ~25 micrometers accuracy, which is aided by a camera focused on the crystal. The most common type of goniometer is the "kappa goniometer", which offers three angles of rotation: the ω angle, which rotates about an axis perpendicular to the beam; the κ angle, about an axis at ~50° to the ω axis; and, finally, the φ angle about the loop/capillary axis. When the κ angle is zero, the ω and φ axes are aligned. The κ rotation allows for convenient mounting of the crystal, since the arm in which the crystal is mounted may be swung out towards the crystallographer. The oscillations carried out during data collection (mentioned below) involve the ω axis only. An older type of goniometer is the four-circle goniometer, and its relatives such as the six-circle goniometer.
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| ====X-ray sources====
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| {{further2|[[Diffractometer]] and [[synchrotron light source|Synchrotron]]}}
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| The mounted crystal is then irradiated with a beam of [[Monochrome|monochromatic]] X-rays. The brightest and most useful X-ray sources are [[synchrotron light source|synchrotron]]s; their much higher luminosity allows for better resolution. They also make it convenient to tune the wavelength of the radiation, which is useful for [[multi-wavelength anomalous dispersion]] (MAD) phasing, described below. Synchrotrons are generally national facilities, each with several dedicated [[beamline#Synchrotron radiation beamline|beamline]]s where data is collected around the clock, seven days a week.
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| [[File:X Ray Diffractometer.JPG|thumb|A diffractometer]]
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| Smaller, [[X-ray generator]]s are often used in laboratories to check the quality of crystals before bringing them to a synchrotron and sometimes to solve a crystal structure. In such systems, electrons are boiled off of a cathode and accelerated through a strong electric potential of ~50 [[Volt|kV]]; having reached a high speed, the electrons collide with a metal plate, emitting ''[[bremsstrahlung]]'' and some strong spectral lines corresponding to the excitation of [[Atomic orbital|inner-shell electrons]] of the metal. The most common metal used is [[copper]], which can be kept cool easily, due to its high [[thermal conductivity]], and which produces strong [[K-alpha|K<sub>α</sub>]] and K<sub>β</sub> lines. The K<sub>β</sub> line is sometimes suppressed with a thin (~10 µm) nickel foil. The simplest and cheapest variety of sealed X-ray tube has a stationary anode (the [[Crookes tube]]) and run with ~2 [[Watt#Kilowatt|kW]] of electron beam power. The more expensive variety has a [[X-ray tube#Rotating anode tube|rotating-anode type source]] that run with ~14 kW of e-beam power.
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| X-rays are generally filtered (by use of [[X-Ray Filters]]) to a single wavelength (made monochromatic) and [[collimator|collimated]] to a single direction before they are allowed to strike the crystal. The filtering not only simplifies the data analysis, but also removes radiation that degrades the crystal without contributing useful information. Collimation is done either with a collimator (basically, a long tube) or with a clever arrangement of gently curved mirrors. Mirror systems are preferred for small crystals (under 0.3 mm) or with large unit cells (over 150 Å)
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| ====Recording the reflections====
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| [[File:X-ray diffraction pattern 3clpro.jpg|thumb|An X-ray diffraction pattern of a crystallized enzyme. The pattern of spots (''reflections'') and the relative strength of each spot (''intensities'') can be used to determine the structure of the enzyme.]]
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| When a crystal is mounted and exposed to an intense beam of X-rays, it scatters the X-rays into a pattern of spots or ''reflections'' that can be observed on a screen behind the crystal. A similar pattern may be seen by shining a [[laser pointer]] at a [[compact disc]]. The relative intensities of these spots provide the information to determine the arrangement of molecules within the crystal in atomic detail. The intensities of these reflections may be recorded with [[photographic film]], an area detector or with a [[charge-coupled device]] (CCD) image sensor. The peaks at small angles correspond to low-resolution data, whereas those at high angles represent high-resolution data; thus, an upper limit on the eventual resolution of the structure can be determined from the first few images. Some measures of diffraction quality can be determined at this point, such as the mosaicity of the crystal and its overall disorder, as observed in the peak widths. Some pathologies of the crystal that would render it unfit for solving the structure can also be diagnosed quickly at this point.
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| One image of spots is insufficient to reconstruct the whole crystal; it represents only a small slice of the full Fourier transform. To collect all the necessary information, the crystal must be rotated step-by-step through 180°, with an image recorded at every step; actually, slightly more than 180° is required to cover reciprocal space, due to the curvature of the [[Ewald sphere]]. However, if the crystal has a higher symmetry, a smaller angular range such as 90° or 45° may be recorded. The rotation axis should be changed at least once, to avoid developing a "blind spot" in reciprocal space close to the rotation axis. It is customary to rock the crystal slightly (by 0.5–2°) to catch a broader region of reciprocal space.
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| Multiple data sets may be necessary for certain phasing methods. For example, MAD phasing requires that the scattering be recorded at least three (and usually four, for redundancy) wavelengths of the incoming X-ray radiation. A single crystal may degrade too much during the collection of one data set, owing to radiation damage; in such cases, data sets on multiple crystals must be taken.<ref>{{cite journal|author=Ravelli RB, Garman EF|title=Radiation damage in macromolecular cryocrystallography|journal=Curr. Opin. Struct. Biol.|volume=16|year=2006|pmid=16938450|doi=10.1016/j.sbi.2006.08.001|issue=5|pages=624–9}}</ref>
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| ===Data analysis===
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| ====Crystal symmetry, unit cell, and image scaling====
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| {{further2|[[Space group]]}}
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| The recorded series of two-dimensional diffraction patterns, each corresponding to a different crystal orientation, is converted into a three-dimensional model of the electron density; the conversion uses the mathematical technique of Fourier transforms, which is explained [[#Diffraction theory|below]]. Each spot corresponds to a different type of variation in the electron density; the crystallographer must determine ''which'' variation corresponds to ''which'' spot (''indexing''), the relative strengths of the spots in different images (''merging and scaling'') and how the variations should be combined to yield the total electron density (''phasing'').
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| Data processing begins with ''indexing'' the reflections. This means identifying the dimensions of the unit cell and which image peak corresponds to which position in reciprocal space. A byproduct of indexing is to determine the symmetry of the crystal, i.e., its ''[[space group]]''. Some space groups can be eliminated from the beginning. For example, reflection symmetries cannot be observed in chiral molecules; thus, only 65 space groups of 230 possible are allowed for protein molecules which are almost always chiral. Indexing is generally accomplished using an ''autoindexing'' routine.<ref>{{cite journal|author=Powell HR|title=The Rossmann Fourier autoindexing algorithm in MOSFLM|journal=Acta Crystallographica D|volume=55|year=1999|pmid=10531518|doi=10.1107/S0907444999009506|issue=Pt 10|pages=1690–5}}</ref> Having assigned symmetry, the data is then ''integrated''. This converts the hundreds of images containing the thousands of reflections into a single file, consisting of (at the very least) records of the [[Miller index]] of each reflection, and an intensity for each reflection (at this state the file often also includes error estimates and measures of partiality (what part of a given reflection was recorded on that image)).
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| A full data set may consist of hundreds of separate images taken at different orientations of the crystal. The first step is to merge and scale these various images, that is, to identify which peaks appear in two or more images (''merging'') and to scale the relative images so that they have a consistent intensity scale. Optimizing the intensity scale is critical because the relative intensity of the peaks is the key information from which the structure is determined. The repetitive technique of crystallographic data collection and the often high symmetry of crystalline materials cause the diffractometer to record many symmetry-equivalent reflections multiple times. This allows calculating the symmetry-related [[R-factor (crystallography)|R-factor]], a reliability index based upon how similar are the measured intensities of symmetry-equivalent reflections, thus assessing the quality of the data.
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| ====Initial phasing====
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| {{further2|[[Phase problem]]}}
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| The data collected from a diffraction experiment is a [[reciprocal space]] representation of the crystal lattice. The position of each diffraction 'spot' is governed by the size and shape of the unit cell, and the inherent [[Unit cell|symmetry]] within the crystal. The intensity of each diffraction 'spot' is recorded, and this intensity is proportional to the square of the ''structure factor'' [[amplitude]]. The [[structure factor]] is a [[complex number]] containing information relating to both the [[amplitude]] and [[Phase (waves)|phase]] of a [[wave]]. In order to obtain an interpretable ''electron density map'', both amplitude and phase must be known (an electron density map allows a crystallographer to build a starting model of the molecule). The phase cannot be directly recorded during a diffraction experiment: this is known as the [[phase problem]]. Initial phase estimates can be obtained in a variety of ways:
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| * '''''[[Ab initio]]'' phasing''' or '''[[Direct methods (crystallography)|direct methods]]''' – This is usually the method of choice for small molecules (<1000 non-hydrogen atoms), and has been used successfully to solve the phase problems for small proteins. If the resolution of the data is better than 1.4 Å (140 [[picometre|pm]]), [[Direct methods (crystallography)|direct methods]] can be used to obtain phase information, by exploiting known phase relationships between certain groups of reflections.<ref>{{cite journal|author=Hauptman H|title=Phasing methods for protein crystallography|journal=Curr. Opin. Struct. Biol.|volume=7|year=1997|pmid=9345626|doi=10.1016/S0959-440X(97)80077-2|issue=5|pages=672–80}}</ref><ref>{{cite journal|author=Usón I, Sheldrick GM|title=Advances in direct methods for protein crystallography|journal=Curr. Opin. Struct. Biol.|volume=9|year=1999|pmid=10508770|doi=10.1016/S0959-440X(99)00020-2|issue=5|pages=643–8}}</ref>
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| * '''[[Molecular replacement]]''' – if a related structure is known, it can be used as a search model in molecular replacement to determine the orientation and position of the molecules within the unit cell. The phases obtained this way can be used to generate ''electron density maps''.<ref name=Taylor>{{cite journal|author=Taylor G|title=The phase problem|journal=Acta Crystallographica D|volume=59|page=1881|year=2003|doi=10.1107/S0907444903017815|issue=11}}</ref>
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| * '''[[Anomalous X-ray scattering]]''' (''[[Multi-wavelength anomalous dispersion|MAD]] or [[Single wavelength anomalous dispersion|SAD phasing]]'') – the X-ray wavelength may be scanned past an absorption edge of an atom, which changes the scattering in a known way. By recording full sets of reflections at three different wavelengths (far below, far above and in the middle of the absorption edge) one can solve for the substructure of the anomalously diffracting atoms and thence the structure of the whole molecule. The most popular method of incorporating anomalous scattering atoms into proteins is to express the protein in a [[methionine]] auxotroph (a host incapable of synthesizing methionine) in a media rich in seleno-methionine, which contains [[selenium]] atoms. A MAD experiment can then be conducted around the absorption edge, which should then yield the position of any methionine residues within the protein, providing initial phases.<ref>{{cite journal|author=Ealick SE|title=Advances in multiple wavelength anomalous diffraction crystallography|journal=Current Opinion in Chemical Biology|volume=4|year=2000|pmid=11006535|doi=10.1016/S1367-5931(00)00122-8|issue=5|pages=495–9}}</ref>
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| * '''Heavy atom methods''' ([[multiple isomorphous replacement]]) – If electron-dense metal atoms can be introduced into the crystal, [[Direct methods (crystallography)|direct methods]] or [[Patterson function|Patterson-space methods]] can be used to determine their location and to obtain initial phases. Such heavy atoms can be introduced either by soaking the crystal in a heavy atom-containing solution, or by co-crystallization (growing the crystals in the presence of a heavy atom). As in MAD phasing, the changes in the scattering amplitudes can be interpreted to yield the phases. Although this is the original method by which protein crystal structures were solved, it has largely been superseded by MAD phasing with selenomethionine.<ref name=Taylor/>
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| ====Model building and phase refinement====
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| [[File:eden.png|thumb|A [[protein]] crystal structure at 2.7 Å resolution. The mesh encloses the region in which the electron density exceeds a given threshold. The straight segments represent chemical bonds between the non-hydrogen atoms of an [[arginine]] (upper left), a [[tyrosine]] (lower left), a [[disulfide bond]] (upper right, in yellow), and some [[peptide|peptide groups]] (running left-right in the middle). The two curved green tubes represent [[spline (mathematics)|spline]] fits to the polypeptide backbone.]]
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| {{further2|[[Molecular modelling|Molecular modeling]]}}
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| Having obtained initial phases, an initial model can be built. This model can be used to refine the phases, leading to an improved model, and so on. Given a model of some atomic positions, these positions and their respective [[Debye-Waller factor]]s (or '''B'''-factors, accounting for the thermal motion of the atom) can be refined to fit the observed diffraction data, ideally yielding a better set of phases. A new model can then be fit to the new electron density map and a further round of refinement is carried out. This continues until the correlation between the diffraction data and the model is maximized. The agreement is measured by an [[R-factor (crystallography)|''R''-factor]] defined as
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| :<math>R = \frac{\sum_{\mathrm{all\ reflections}} \left|F_{o} - F_{c} \right|}{\sum_{\mathrm{all\ reflections}} \left|F_{o} \right|}</math>
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| where ''F'' is the [[structure factor]]. A similar quality criterion is ''R''<sub>free</sub>, which is calculated from a subset (~10%) of reflections that were not included in the structure refinement. Both ''R'' factors depend on the resolution of the data. As a rule of thumb, ''R''<sub>free</sub> should be approximately the resolution in angstroms divided by 10; thus, a data-set with 2 Å resolution should yield a final ''R''<sub>free</sub> ~ 0.2. Chemical bonding features such as stereochemistry, hydrogen bonding and distribution of bond lengths and angles are complementary measures of the model quality. Phase bias is a serious problem in such iterative model building. ''Omit maps'' are a common technique used to check for this.{{Clarify|date=February 2009}}
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| It may not be possible to observe every atom of the crystallized molecule – it must be remembered that the resulting electron density is an average of all the molecules within the crystal. In some cases, there is too much residual disorder in those atoms, and the resulting electron density for atoms existing in many conformations is smeared to such an extent that it is no longer detectable in the electron density map. Weakly scattering atoms such as hydrogen are routinely invisible. It is also possible for a single atom to appear multiple times in an electron density map, e.g., if a protein sidechain has multiple (<4) allowed conformations. In still other cases, the crystallographer may detect that the covalent structure deduced for the molecule was incorrect, or changed. For example, proteins may be cleaved or undergo post-translational modifications that were not detected prior to the crystallization.
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| ===Deposition of the structure===
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| Once the model of a molecule's structure has been finalized, it is often deposited in a [[crystallographic database]] such as the [[Cambridge Structural Database]] (for small molecules), the [[Inorganic Crystal Structure Database (ICSD)]] (for inorganic compounds) or the [[Protein Data Bank]] (for protein structures). Many structures obtained in private commercial ventures to crystallize medicinally relevant proteins are not deposited in public crystallographic databases.
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| ==Diffraction theory==
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| {{further2|[[Dynamical theory of diffraction]] and [[Bragg diffraction]]}}
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| The main goal of X-ray crystallography is to determine the density of electrons ''f''('''r''') throughout the crystal, where '''r''' represents the three-dimensional position [[vector (geometry)|vector]] within the crystal. To do this, X-ray scattering is used to collect data about its Fourier transform ''F''('''q'''), which is inverted mathematically to obtain the density defined in real space, using the formula
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| :<math>f(\mathbf{r}) = \frac{1}{\left(2\pi\right)^{3}} \int F(\mathbf{q}) e^{\mathrm{i}\mathbf{q}\cdot\mathbf{r}} \mathrm{d}\mathbf{q}</math>
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| where the [[integral]] is taken over all values of '''q'''. The three-dimensional real vector '''q''' represents a point in [[reciprocal space]], that is, to a particular oscillation in the electron density as one moves in the direction in which '''q''' points. The length of '''q''' corresponds to 2<math>\pi</math> divided by the wavelength of the oscillation. The corresponding formula for a Fourier transform will be used below
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| :<math>F(\mathbf{q}) = \int f(\mathbf{r}) \mathrm{e}^{-\mathrm{i}\mathbf{q}\cdot\mathbf{r}}\mathrm{d}\mathbf{r}</math>
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| where the [[integral]] is summed over all possible values of the position vector '''r''' within the crystal.
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| The Fourier transform ''F''('''q''') is generally a [[complex number]], and therefore has a [[magnitude (mathematics)|magnitude]] |''F''('''q''')| and a [[Phase (waves)|phase]] ''φ''('''q''') related by the equation
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| :<math>F(\mathbf{q}) = \left|F(\mathbf{q}) \right|\mathrm{e}^{\mathrm{i}\phi(\mathbf{q})}</math>
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| The intensities of the reflections observed in X-ray diffraction give us the magnitudes |''F''('''q''')| but not the phases ''φ''('''q'''). To obtain the phases, full sets of reflections are collected with known alterations to the scattering, either by modulating the wavelength past a certain absorption edge or by adding strongly scattering (i.e., electron-dense) metal atoms such as [[mercury (element)|mercury]]. Combining the magnitudes and phases yields the full Fourier transform ''F''('''q'''), which may be inverted to obtain the electron density ''f''('''r''').
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| Crystals are often idealized as being ''perfectly'' periodic. In that ideal case, the atoms are positioned on a perfect lattice, the electron density is perfectly periodic, and the Fourier transform ''F''('''q''') is zero except when '''q''' belongs to the [[reciprocal lattice]] (the so-called ''Bragg peaks''). In reality, however, crystals are not perfectly periodic; atoms vibrate about their mean position, and there may be disorder of various types, such as mosaicity, dislocations, various point defects, and heterogeneity in the conformation of crystallized molecules. Therefore, the Bragg peaks have a finite width and there may be significant ''diffuse scattering'', a continuum of scattered X-rays that fall between the Bragg peaks.
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| ===Intuitive understanding by Bragg's law===
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| An intuitive understanding of X-ray diffraction can be obtained from the [[Bragg diffraction|Bragg model of diffraction]]. In this model, a given reflection is associated with a set of evenly spaced sheets running through the crystal, usually passing through the centers of the atoms of the crystal lattice. The orientation of a particular set of sheets is identified by its [[Miller index|three Miller indices]] (''h'', ''k'', ''l''), and let their spacing be noted by ''d''. William Lawrence Bragg proposed a model in which the incoming X-rays are scattered specularly (mirror-like) from each plane; from that assumption, X-rays scattered from adjacent planes will combine constructively ([[constructive interference]]) when the angle θ between the plane and the X-ray results in a path-length difference that is an integer multiple ''n'' of the X-ray wavelength λ.
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| :<math>2 d\sin\theta = n\lambda\,</math>
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| A reflection is said to be ''indexed'' when its Miller indices (or, more correctly, its [[reciprocal lattice]] vector components) have been identified from the known wavelength and the scattering angle 2θ. Such indexing gives the [[lattice parameter|unit-cell parameters]], the lengths and angles of the unit-cell, as well as its [[space group]]. Since [[Bragg's law]] does not interpret the relative intensities of the reflections, however, it is generally inadequate to solve for the arrangement of atoms within the unit-cell; for that, a Fourier transform method must be carried out.
| |
| | |
| ===Scattering as a Fourier transform===
| |
| The incoming X-ray beam has a polarization and should be represented as a vector wave; however, for simplicity, let it be represented here as a scalar wave. We also ignore the complication of the time dependence of the wave and just focus on the wave's spatial dependence. [[Plane wave]]s can be represented by a [[wave vector]] '''k'''<sub>in</sub>, and so the strength of the incoming wave at time ''t=0'' is given by
| |
| :<math>A \mathrm{e}^{\mathrm{i}\mathbf{k}_{\mathrm{in}} \cdot \mathbf{r}}</math>
| |
| | |
| At position '''r''' within the sample, let there be a density of scatterers ''f''('''r'''); these scatterers should produce a scattered spherical wave of amplitude proportional to the local amplitude of the incoming wave times the number of scatterers in a small volume ''dV'' about '''r'''
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| :<math>\mathrm{amplitude\ of\ scattered\ wave} = A \mathrm{e}^{\mathrm{i}\mathbf{k} \cdot \mathbf{r}} S f(\mathbf{r}) \mathrm{d}V</math>
| |
| where ''S'' is the proportionality constant.
| |
| | |
| Let's consider the fraction of scattered waves that leave with an outgoing wave-vector of '''k'''<sub>out</sub> and strike the screen at '''r'''<sub>screen</sub>. Since no energy is lost (elastic, not inelastic scattering), the wavelengths are the same as are the magnitudes of the wave-vectors |'''k'''<sub>in</sub>|=|'''k'''<sub>out</sub>|. From the time that the photon is scattered at '''r''' until it is absorbed at '''r'''<sub>screen</sub>, the photon undergoes a change in phase
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| :<math>e^{i \mathbf{k}_{out} \cdot \left( \mathbf{r}_{\mathrm{screen}} - \mathbf{r} \right)}</math>
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| | |
| The net radiation arriving at '''r'''<sub>screen</sub> is the sum of all the scattered waves throughout the crystal
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| :<math>A S \int \mathrm{d}\mathbf{r} f(\mathbf{r}) \mathrm{e}^{\mathrm{i} \mathbf{k}_{in} \cdot \mathbf{r}} | |
| e^{i \mathbf{k}_{out} \cdot \left( \mathbf{r}_{\mathrm{screen}} - \mathbf{r} \right)} =
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| A S e^{i \mathbf{k}_{out} \cdot \mathbf{r}_{\mathrm{screen}}}
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| \int \mathrm{d}\mathbf{r} f(\mathbf{r}) \mathrm{e}^{\mathrm{i} \left( \mathbf{k}_{in} - \mathbf{k}_{out} \right) \cdot \mathbf{r}} </math>
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| | |
| which may be written as a Fourier transform
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| :<math>A S \mathrm{e}^{\mathrm{i} \mathbf{k}_{out} \cdot \mathbf{r}_{\mathrm{screen}}} | |
| \int d\mathbf{r} f(\mathbf{r}) \mathrm{e}^{-\mathrm{i} \mathbf{q} \cdot \mathbf{r}} =
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| A S \mathrm{e}^{\mathrm{i} \mathbf{k}_{out} \cdot \mathbf{r}_{\mathrm{screen}}} F(\mathbf{q})</math>
| |
| | |
| where '''q''' = '''k'''<sub>out</sub> – '''k'''<sub>in</sub>. The measured intensity of the reflection will be square of this amplitude
| |
| :<math>A^{2} S^{2} \left|F(\mathbf{q}) \right|^{2}</math>
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| | |
| ===Friedel and Bijvoet mates===
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| For every reflection corresponding to a point '''q''' in the reciprocal space, there is another reflection of the same [[intensity (physics)|intensity]] at the opposite point -'''q'''. This opposite reflection is known as the ''Friedel mate'' of the original reflection. This symmetry results from the mathematical fact that the density of electrons ''f''('''r''') at a position '''r''' is always a [[real number]]. As noted above, ''f''('''r''') is the inverse transform of its Fourier transform ''F''('''q'''); however, such an inverse transform is a [[complex number]] in general. To ensure that ''f''('''r''') is real, the Fourier transform ''F''('''q''') must be such that the Friedel mates ''F''(−'''q''') and ''F''('''q''') are [[complex conjugate]]s of one another. Thus, ''F''(−'''q''') has the same magnitude as ''F''('''q''') but they have the opposite phase, i.e., ''φ''('''q''') = −''φ''('''q''')
| |
| :<math>F(-\mathbf{q}) = \left|F(-\mathbf{q}) \right|\mathrm{e}^{\mathrm{i}\phi(-\mathbf{q})} = F^{*}(\mathbf{q}) = \left| F(\mathbf{q}) \right|\mathrm{e}^{-\mathrm{i}\phi(\mathbf{q})} </math>
| |
| | |
| The equality of their magnitudes ensures that the Friedel mates have the same intensity |''F''|<sup>2</sup>. This symmetry allows one to measure the full Fourier transform from only half the reciprocal space, e.g., by rotating the crystal slightly more than 180° instead of a full 360° revolution. In crystals with significant symmetry, even more reflections may have the same intensity (Bijvoet mates); in such cases, even less of the reciprocal space may need to be measured. In favorable cases of high symmetry, sometimes only 90° or even only 45° of data are required to completely explore the reciprocal space.
| |
| | |
| The Friedel-mate constraint can be derived from the definition of the inverse Fourier transform
| |
| :<math>f(\mathbf{r}) = \int \frac{d\mathbf{q}}{\left(2\pi\right)^{3}} F(\mathbf{q}) \mathrm{e}^{\mathrm{i}\mathbf{q}\cdot\mathbf{r}} =
| |
| \int \frac{d\mathbf{q}}{\left(2\pi\right)^{3}} \left|F(\mathbf{q}) \right|\mathrm{e}^{\mathrm{i}\phi(\mathbf{q})} \mathrm{e}^{\mathrm{i}\mathbf{q}\cdot\mathbf{r}} </math>
| |
| | |
| Since [[Euler's formula]] states that e<sup>i''x''</sup> = cos(''x'') + i sin(''x''), the inverse Fourier transform can be separated into a sum of a purely real part and a purely imaginary part
| |
| :<math>f(\mathbf{r}) =
| |
| \int \frac{d\mathbf{q}}{\left(2\pi\right)^{3}} \left|F(\mathbf{q}) \right|\mathrm{e}^{\mathrm{i}\left(\phi+\mathbf{q}\cdot\mathbf{r}\right)} =
| |
| \int \frac{d\mathbf{q}}{\left(2\pi\right)^{3}} \left|F(\mathbf{q}) \right|
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| \cos\left(\phi+\mathbf{q}\cdot\mathbf{r}\right) +
| |
| i \int \frac{d\mathbf{q}}{\left(2\pi\right)^{3}} \left|F(\mathbf{q}) \right|
| |
| \sin\left(\phi+\mathbf{q}\cdot\mathbf{r}\right) = I_{\mathrm{cos}} + iI_{\mathrm{sin}}</math>
| |
| | |
| The function ''f''('''r''') is real if and only if the second integral ''I''<sub>sin</sub> is zero for all values of '''r'''. In turn, this is true if and only if the above constraint is satisfied
| |
| :<math>I_{\mathrm{sin}} = \int \frac{d\mathbf{q}}{\left(2\pi\right)^{3}} \left|F(\mathbf{q}) \right|\sin\left(\phi+\mathbf{q}\cdot\mathbf{r}\right) =
| |
| \int \frac{d\mathbf{q}}{\left(2\pi\right)^{3}} \left|F(\mathbf{-q}) \right|
| |
| \sin\left(-\phi-\mathbf{q}\cdot\mathbf{r}\right) = -I_{\mathrm{sin}}</math>
| |
| | |
| since ''I''<sub>sin</sub> = −''I''<sub>sin</sub> implies that ''I''<sub>sin</sub>=0.
| |
| | |
| ===Ewald's sphere===
| |
| {{further2|[[Ewald's sphere]]}}
| |
| Each X-ray diffraction image represents only a slice, a spherical slice of reciprocal space, as may be seen by the Ewald sphere construction. Both '''k'''<sub>out</sub> and '''k'''<sub>in</sub> have the same length, due to the elastic scattering, since the wavelength has not changed. Therefore, they may be represented as two radial vectors in a sphere in [[reciprocal space]], which shows the values of '''q''' that are sampled in a given diffraction image. Since there is a slight spread in the incoming wavelengths of the incoming X-ray beam, the values of|''F''('''q''')|can be measured only for '''q''' vectors located between the two spheres corresponding to those radii. Therefore, to obtain a full set of Fourier transform data, it is necessary to rotate the crystal through slightly more than 180°, or sometimes less if sufficient symmetry is present. A full 360° rotation is not needed because of a symmetry intrinsic to the Fourier transforms of real functions (such as the electron density), but "slightly more" than 180° is needed to cover all of reciprocal space within a given resolution because of the curvature of the [[Ewald sphere]]. In practice, the crystal is rocked by a small amount (0.25-1°) to incorporate reflections near the boundaries of the spherical Ewald shells.
| |
| | |
| ===Patterson function===
| |
| {{further2|[[Patterson function]]}}
| |
| A well-known result of Fourier transforms is the [[autocorrelation]] theorem, which states that the autocorrelation ''c''('''r''') of a function ''f''('''r''')
| |
| :<math>c(\mathbf{r}) = \int d\mathbf{x} f(\mathbf{x}) f(\mathbf{x} + \mathbf{r}) = \int \frac{d\mathbf{q}}{\left(2\pi\right)^{3}} C(\mathbf{q}) e^{i\mathbf{q}\cdot\mathbf{r}}</math>
| |
| | |
| has a Fourier transform ''C''('''q''') that is the squared magnitude of ''F''('''q''')
| |
| :<math>C(\mathbf{q}) = \left|F(\mathbf{q}) \right|^{2}</math>
| |
| | |
| Therefore, the autocorrelation function ''c''('''r''') of the electron density (also known as the ''Patterson function''<ref>{{cite journal|author=Patterson AL|authorlink=Arthur Lindo Patterson|year = 1935|title=A Direct Method for the Determination of the Components of Interatomic Distances in Crystals|journal=Zeitschrift für Kristallographie|volume=90|page=517}}</ref>) can be computed directly from the reflection intensities, without computing the phases. In principle, this could be used to determine the crystal structure directly; however, it is difficult to realize in practice. The autocorrelation function corresponds to the distribution of [[vector (geometry)|vectors]] between atoms in the crystal; thus, a crystal of ''N'' atoms in its unit cell may have ''N(N-1)'' peaks in its Patterson function. Given the inevitable errors in measuring the intensities, and the mathematical difficulties of reconstructing atomic positions from the interatomic vectors, this technique is rarely used to solve structures, except for the simplest crystals.
| |
| | |
| ===Advantages of a crystal===
| |
| In principle, an atomic structure could be determined from applying X-ray scattering to non-crystalline samples, even to a single molecule. However, crystals offer a much stronger signal due to their periodicity. A crystalline sample is by definition periodic; a crystal is composed of many [[unit cell]]s repeated indefinitely in three independent directions. Such periodic systems have a [[Fourier transform]] that is concentrated at periodically repeating points in reciprocal space known as ''Bragg peaks''; the Bragg peaks correspond to the reflection spots observed in the diffraction image. Since the amplitude at these reflections grows linearly with the number ''N'' of scatterers, the observed ''intensity'' of these spots should grow quadratically, like ''N''<sup>2</sup>. In other words, using a crystal concentrates the weak scattering of the individual unit cells into a much more powerful, coherent reflection that can be observed above the noise. This is an example of [[constructive interference]].
| |
| | |
| In a liquid, powder or amorphous sample, molecules within that sample are in random orientations. Such samples have a continuous Fourier spectrum that uniformly spreads its amplitude thereby reducing the measured signal intensity, as is observed in [[Biological Small-Angle X-ray Scattering|SAXS]]. More importantly, the orientational information is lost. Although theoretically possible, it is experimentally difficult to obtain atomic-resolution structures of complicated, asymmetric molecules from such rotationally averaged data. An intermediate case is [[fiber diffraction]] in which the subunits are arranged periodically in at least one dimension.
| |
| | |
| ==See also==
| |
| {{Multicol}}
| |
| * [[Bragg diffraction]]
| |
| * [[Bravais lattice]]
| |
| * [[Crystallographic database]]
| |
| * [[Crystallographic point groups]]
| |
| * [[Difference density map]]
| |
| * [[Electron crystallography]]
| |
| * [[Electron diffraction]]
| |
| * [[Henderson limit]]
| |
| * [[International Year of Crystallography]]
| |
| {{Multicol-break}}
| |
| * [[Neutron diffraction]]
| |
| * [[Powder diffraction]]
| |
| * [[Energy Dispersive X-Ray Diffraction]]
| |
| * [[Ptychography]]
| |
| * [[Scherrer equation]]
| |
| * [[Small angle X-ray scattering (SAXS)]]
| |
| * [[Structure determination]]
| |
| * [[Ultrafast x-rays]]
| |
| * [[Wide angle X-ray scattering]] (WAXS)
| |
| {{Multicol-break}}
| |
| * [[Max von Laue]]
| |
| * [[John Desmond Bernal]]
| |
| * [[William Henry Bragg]]
| |
| * [[William Lawrence Bragg]]
| |
| * [[Rosalind Franklin]]
| |
| * [[Dorothy Hodgkin]]
| |
| * [[John Kendrew]]
| |
| * [[Max Perutz]]
| |
| {{Multicol-end}}
| |
| | |
| ==References==
| |
| {{Reflist|2}}
| |
| | |
| ==Further reading==
| |
| | |
| ===''International Tables for Crystallography''===
| |
| * {{cite book|year=2002|title=International Tables for Crystallography. Volume A, Space-group Symmetry|edition = 5|publisher=[[Kluwer Academic Publishers]], for the [[International Union of Crystallography]]|location=Dordrecht|isbn=0-7923-6590-9|editor=Theo Hahn}}
| |
| * {{cite book|year=2001|title=International Tables for Crystallography. Volume F, Crystallography of biological molecules|editor = Michael G. Rossmann and Eddy Arnold|publisher=Kluwer Academic Publishers, for the International Union of Crystallography|location=Dordrecht|isbn = 0-7923-6857-6}}
| |
| * {{cite book|year=1996|title=International Tables for Crystallography. Brief Teaching Edition of Volume A, Space-group Symmetry|edition = 4|publisher=Kluwer Academic Publishers, for the International Union of Crystallography|location=Dordrecht|isbn=0-7923-4252-6|editor=Theo Hahn}}
| |
| | |
| ===Bound collections of articles===
| |
| * {{cite book|year=1997|title=Macromolecular Crystallography, Part A (Methods in Enzymology, v. 276)|publisher=Academic Press|location=San Diego|isbn=0-12-182177-3|editor=Charles W. Carter and Robert M. Sweet.}}
| |
| * {{cite book|year=1997|title=Macromolecular Crystallography, Part B (Methods in Enzymology, v. 277)|publisher=Academic Press|location=San Diego|isbn=0-12-182178-1|editor=Charles W. Carter Jr., Robert M. Sweet.}}
| |
| * {{cite book|year=1999|title=Crystallization of Nucleic Acids and Proteins: A Practical Approach|edition = 2|editor=A. Ducruix and R. Giegé|publisher=Oxford University Press|location=Oxford|isbn=0-19-963678-8}}
| |
| | |
| ===Textbooks===
| |
| * {{cite book|author=B.E. Warren|year=1969|title=X-ray Diffraction|location=New York|isbn=0486663175}}
| |
| * {{cite book|author=Blow D|year=2002|title=Outline of Crystallography for Biologists|publisher=Oxford University Press|location=Oxford|isbn=0-19-851051-9}}
| |
| * {{cite book|author=Burns G., Glazer A M|year=1990|title=Space Groups for Scientists and Engineers|edition = 2nd|location=Boston
| |
| |publisher=Academic Press, Inc|isbn=0-12-145761-3}}
| |
| * {{cite book|author=Clegg W|year=1998|title=Crystal Structure Determination (Oxford Chemistry Primer)|publisher=Oxford University Press|location=Oxford|isbn=0-19-855901-1}}
| |
| * {{cite book|author=Cullity B.D.|year=1978|title=Elements of X-Ray Diffraction|edition = 2nd|publisher=Addison-Wesley Publishing Company|location=Reading, Massachusetts|isbn=0-534-55396-6}}
| |
| * {{cite book|author=Drenth J|year=1999|title=Principles of Protein X-Ray Crystallography|publisher=Springer-Verlag|location=New York|isbn=0-387-98587-5}}
| |
| * {{cite book|author=Giacovazzo C|year=1992|title=Fundamentals of Crystallography|publisher=Oxford University Press|location=Oxford|isbn=0-19-855578-4|author-separator=,|display-authors=1}}
| |
| * {{cite book|author=Glusker JP, Lewis M, Rossi M|year=1994|title=Crystal Structure Analysis for Chemists and Biologists|publisher=VCH Publishers|location=New York|isbn=0-471-18543-4}}
| |
| * {{cite book|author=Massa W|year=2004|title=Crystal Structure Determination|publisher=Springer|location=Berlin|isbn=3-540-20644-2}}
| |
| * {{cite book|author=McPherson A|year=1999|title=Crystallization of Biological Macromolecules|publisher=Cold Spring Harbor Laboratory Press|location=Cold Spring Harbor, NY|isbn =0-87969-617-6}}
| |
| * {{cite book|author=McPherson A|year=2003|title=Introduction to Macromolecular Crystallography|publisher=John Wiley & Sons|isbn=0-471-25122-4}}
| |
| * {{cite book|author=McRee DE|year=1993|title=Practical Protein Crystallography|publisher=Academic Press|location=San Diego|isbn=0-12-486050-8}}
| |
| * {{cite book|author=O'Keeffe M, Hyde B G|year=1996|title=Crystal Structures; I. Patterns and Symmetry|publisher=Mineralogical Society of America, ''Monograph Series''|location=Washington, DC|isbn=0-939950-40-5}}
| |
| * {{cite book|author=Rhodes G|year=2000|title=Crystallography Made Crystal Clear|publisher=Academic Press|location=San Diego|isbn=0-12-587072-8}}, [http://www.chem.uwec.edu/Chem406_F06/Pages/lecture_notes/lect07/Crystallography_Rhodes.pdf PDF copy of select chapters]
| |
| * {{cite book|author=Rupp B|year=2009|title=Biomolecular Crystallography: Principles, Practice and Application to Structural Biology|publisher=Garland Science|location=New York|isbn=0-8153-4081-8}}
| |
| * {{cite book|author=Zachariasen WH|year=1945|title=Theory of X-ray Diffraction in Crystals|publisher=Dover Publications|location=New York|lccn=6726967}}
| |
| | |
| ===Applied computational data analysis===
| |
| * {{cite book|editor = Young, R.A.|year=1993|title=The Rietveld Method|location=Oxford|publisher=Oxford University Press & International Union of Crystallography|isbn=0-19-855577-6}}
| |
| | |
| ===Historical===
| |
| * {{cite book|author=[[Johannes Martin Bijvoet|Bijvoet JM]], Burgers WG, Hägg G, eds.|year=1969|title=Early Papers on Diffraction of X-rays by Crystals (Volume I)|publisher=published for the International Union of Crystallography by A. Oosthoek's Uitgeversmaatschappij N.V.|location=Utrecht}}
| |
| * {{cite book|author=Bijvoet JM, Burgers WG, Hägg G, eds.|year=1972|title=Early Papers on Diffraction of X-rays by Crystals (Volume II)|publisher=published for the International Union of Crystallography by A. Oosthoek's Uitgeversmaatschappij N.V.|location=Utrecht}}
| |
| * {{cite book|author=Bragg W L, Phillips D C and Lipson H|year=1992|title=The Development of X-ray Analysis|publisher=Dover|location=New York|isbn=0-486-67316-2}}
| |
| * {{cite book|author=[[Paul Peter Ewald|Ewald PP]], editor, and numerous crystallographers|year=1962|title=Fifty Years of X-ray Diffraction|publisher=published for the International Union of Crystallography by A. Oosthoek's Uitgeversmaatschappij N.V.|location=Utrecht}}
| |
| * Ewald, P. P., editor [http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/ ''50 Years of X-Ray Diffraction''] (Reprinted in pdf format for the IUCr XVIII Congress, Glasgow, Scotland, International Union of Crystallography).
| |
| * {{cite journal|author=Friedrich W|year=1922|title=Die Geschichte der Auffindung der Röntgenstrahlinterferenzen|journal=Die Naturwissenschaften|volume=10|page=363|doi=10.1007/BF01565289|issue=16|bibcode = 1922NW.....10..363F }}
| |
| * {{cite book|author=Lonsdale, K|year=1949|title=Crystals and X-rays|publisher=D. van Nostrand|location=New York}}
| |
| *{{cite journal|year=2007|title=The Structures of Life|publisher=U.S. Department of Health and Human Services}}
| |
| | |
| ==External links==
| |
| {{Library resources box
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| |onlinebooks=no
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| |by=no
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| |lcheading=X-ray crystallography}}
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| {{wikibooks|Xray Crystallography}}
| |
| | |
| ===Tutorials===
| |
| * [http://www.xtal.iqfr.csic.es/Cristalografia/index-en.html Learning Crystallography]
| |
| * [http://stein.bioch.dundee.ac.uk/~charlie/index.php?section=1 Simple, non technical introduction]
| |
| *[http://richannel.org/collections/2013/crystallography The Crystallography Collection], video series from the [[Royal Institution]]
| |
| * [http://acaschool.iit.edu/lectures04/JLiangXtal.pdf "Small Molecule Crystalization"] ([[PDF]]) at [[Illinois Institute of Technology]] website
| |
| * [http://iucr.org International Union of Crystallography]
| |
| * [http://www.ruppweb.org/Xray/101index.html Crystallography 101]
| |
| * [http://www.ysbl.york.ac.uk/~cowtan/sfapplet/sfintro.html Interactive structure factor tutorial], demonstrating properties of the diffraction pattern of a 2D crystal.
| |
| * [http://www.ysbl.york.ac.uk/~cowtan/fourier/fourier.html Picturebook of Fourier Transforms], illustrating the relationship between crystal and diffraction pattern in 2D.
| |
| * [http://www.chem.uwec.edu/Chem406_F06/Pages/lectnotes.html#lecture7 Lecture notes on X-ray crystallography and structure determination]
| |
| * [http://nanohub.org/resources/5580 Online lecture on Modern X-ray Scattering Methods for Nanoscale Materials Analysis] by Richard J. Matyi
| |
| *[http://rigb.org/our-history/history-of-research/crystallography-timeline Interactive Crystallography Timeline] from the [[Royal Institution]]
| |
| | |
| ===Primary databases===
| |
| * [[Crystallography open database|Crystallography Open Database]] (COD)
| |
| * [[Protein Data Bank]] (PDB)
| |
| * [http://ndbserver.rutgers.edu/ Nucleic Acid Databank] (NDB)
| |
| * [http://www.ccdc.cam.ac.uk/products/csd/ Cambridge Structural Database] (CSD)
| |
| * [http://www.fiz-karlsruhe.de/icsd.html Inorganic Crystal Structure Database] (ICSD)
| |
| * [http://xpdb.nist.gov:8060/BMCD4/ Biological Macromolecule Crystallization Database] (BMCD)
| |
| | |
| ===Derivative databases===
| |
| * [http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ PDBsum]
| |
| * [http://www.proteopedia.org Proteopedia – the collaborative, 3D encyclopedia of proteins and other molecules]
| |
| * [http://www.rnabase.org/ RNABase]
| |
| * [http://xray.bmc.uu.se/hicup/ HIC-Up database of PDB ligands]
| |
| * [[Structural Classification of Proteins]] database
| |
| * [[CATH|CATH Protein Structure Classification]]
| |
| * [http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html List of transmembrane proteins with known 3D structure]
| |
| * [[Orientations of Proteins in Membranes database]]
| |
| | |
| ===Structural validation===
| |
| * [http://molprobity.biochem.duke.edu/ MolProbity structural validation suite]
| |
| * [https://prosa.services.came.sbg.ac.at/prosa.php ProSA-web]
| |
| * [https://flipper.services.came.sbg.ac.at/ NQ-Flipper] (check for unfavorable rotamers of Asn and Gln residues)
| |
| * [http://www.ebi.ac.uk/dali/ DALI server] (identifies proteins similar to a given protein)
| |
| | |
| {{Protein structure determination}}
| |
| | |
| {{good article}}
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| {{DEFAULTSORT:X-Ray Crystallography}}
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| [[Category:X-ray crystallography| ]]
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| [[Category:Crystallography]]
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| [[Category:Diffraction]]
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| [[Category:X-rays|Crystallography]]
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| [[Category:Protein structure]]
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| [[Category:Protein methods]]
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| [[Category:Synchrotron-related techniques]]
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| [[ar:دراسة البلورات بالأشعة السينية]]
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| [[da:Krystallografi]]
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| [[de:Kristallstrukturanalyse]]
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| [[he:קריסטלוגרפיה באמצעות קרני רנטגן]]
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| [[ja:X線結晶構造解析]]
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| [[pt:Cristalografia de raios X]]
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| [[fi:Röntgenkristallografia]]
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| [[zh:X射线晶体学]]
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