Absolute electrode potential - Revision history

en>Magioladitis: Replace unicode entity nbsp for character [NBSP] (or space) per WP:NBSP + other fixes, replaced: → (14) using AWB (10331)

2014-07-29T15:24:23Z

Replace unicode entity nbsp for character [NBSP] (or space) per WP:NBSP + other fixes, replaced: → (14) using AWB (10331)

← Older revision		Revision as of 17:24, 29 July 2014
Line 1:		Line 1:
	~~'''Multiple isomorphous replacement''' or '''MIR''' is, historically speaking, the most common approach to solving the [[phase problem]] in [[X-ray crystallography]]~~. ~~This method is conducted by soaking the crystal of a sample~~ to ~~be analyzed with a [[heavy atom]] solution or co-crystallization with the heavy atom. The addition of the heavy atom should not affect the crystal formation or [[unit cell]] dimensions~~ in ~~comparison to its native form, hence, they should be [[Isomorphism (crystallography)\|isomorphic]].~~		I like Jewelry making. <br>I also to learn Vietnamese in my spare time.<br><br>Here is my website - [http://naeemzaki.net/games/index.php?task=profile&id=382262 wordpress backup plugin]

	~~Data sets from the native and heavy-atom derivative of the sample are first collected~~. Then the interpretation of the [[Patterson function\|Patterson difference map]] reveals the heavy atom's location in the unit cell. This allows both the [[amplitude]] and the [[Phase (waves)\|phase]] of the atom to be determined. Since the [[structure factor]] of the heavy atom derivative ('''F'''<~~sub~~>ph<~~/sub~~>~~) of the crystal~~ is the vector sum of the lone heavy atom ('''F'''<sub>h</sub>) and the native crystal ('''F'''<sub>p</sub>) then the phase of the native '''F'''<sub>p</sub> and '''F'''<sub>ph</sub> vectors can be solved geometrically.

	~~:<math>\mathbf F_{ph} = \mathbf F_p + \mathbf F_h</math>~~

	~~At least two isomorphous derivatives must be evaluated since using only one will give two possible phases.~~

	~~==Examples==~~
	~~Some examples of heavy atoms used in protein MIR:~~
	*[[Mercury (element)\|Hg]]<sup>2+</sup> ions bind to [[thiol]] groups.
	*[[Uranyl]] salts ([[Uranium dioxide\|UO<sub>2</sub>]] + [[Nitrate\|NO<sub>3</sub>]]) bind between [[carboxyl]] groups in [[Aspartic acid\|Asp]] and [[Glutamic acid\|Glu]]
	*[[Lead\|Pb]] bind to [[Cysteine\|Cys]]
	*[[Platinum(IV) chloride\|PtCl<sub>4</sub><sup>2-</sup>]] ([[ion]]) bind to [[Histidine\|His]]

	~~== See also ==~~
	~~=== Anomalous Dispersion ===~~
	* [[Multi-~~wavelength anomalous dispersion]] (MAD)~~
	* [[Single wavelength anomalous dispersion]] (SAD)

	~~=== Isomorphous Replacement ===~~
	~~Two methods for providing the needed phasing information by introducing heavy atoms into isomorphous crystals:~~
	* Multiple isomorphous replacement (MIR); and
	* [[Single isomorphous replacement with anomalous signal]] (SIRAS)

	~~===Other===~~
	*[[Patterson map]]

	~~== References ==~~
	~~{{reflist}}~~

	~~===Further reading===~~
	*{{cite journal \|author=Hendrickson WA \|year=1985 \|title=Analysis of Protein Structure from Diffraction Measurement at Multiple Wavelengths \|journal=Trans. ACA \|volume=21}}
	*{{cite journal \|author=Karle J \|year=1980 \|title=Some Developments in Anomalous Dispersion for the Structural Investigation of Macromolecular Systems in Biology \|journal=International Journal of Quantum Chemistry: Quantum Biology Symposium \|volume=7 \|pages=357–367}}
	*{{cite journal \|author=Karle J \|year=1989 \|title=Linear Algebraic Analyses of Structures with One Predominant Type of Anomalous Scatterer \|journal=Acta Cryst. \|volume=A45 \|pages=303–307}}
	*{{cite journal \|author=Pahler A, Smith JL, Hendrickson WA \|year=1990 \|title=A Probability Representation for Phase Information from Multiwavelength Anomalous Dispersion \|journal=Acta Cryst. \|volume=A46 \|pages=537–540}}
	*{{cite journal \|author=Terwilliger TC \|year=1994 \|title=MAD Phasing: Bayesian Estimates of FA \|journal=Acta Cryst. \|volume=D50 \|pages=11–16}}
	*{{cite journal \|author=Terwilliger TC \|year=1994 \|title=MAD Phasing: Treatment of Dispersive Differences as Isomorphous Replacement Information \|journal=Acta Cryst. \|volume=D50 \|pages=17–23}}
	*{{cite journal \|author=Fourme R, Shepard W, Kahn R, l'Hermite G, de La Sierra IL \|year=1995 \|title=The Multiwavelength Anomalous Solvent Contrast (MASC) Method in Macrocolecular Crystallography \|journal=J. Synchrotron Rad. \|volume=2 \|pages=36–48 \|doi=10.1107/S0909049594006680}}
	*{{cite journal \|author=de la Fortelle E, Bricogne G \|year=1997 \|title=Maximum-Likelihood Heavy-Atom Parameter Refinement for Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods \|journal=Methods in Enzymology \|volume=276 \|pages=472–494 \|doi=10.1016/S0076-6879(97)76073-7 \|series=Methods in Enzymology \|isbn=978-0-12-182177-7}}
	*{{cite journal \|author=Hendrickson WA, Ogata CM \|year=1997 \|title=Phase Determination from Multiwavelength Anomalous Diffraction Measurements \|journal=Methods in Enzymology \|volume=276 \|pages=494–523 \|doi=10.1016/S0076-6879(97)76074-9 \|series=Methods in Enzymology \|isbn=978-0-12-182177-7}}
	*{{cite journal \|author=Bella J, Rossmann MG \|year=1998 \|title=A General Phasing Algorithm for Multiple MAD and MIR Data \|journal=Acta Cryst. \|volume=D54 \|pages=159–174}}
	*{{cite journal \|author=Guss JM, Merritt EA, Phizackerley RP, Hedman B, Murata M, [[Keith Hodgson\|Hodgson KO]], [[Hans Freeman\|Freeman HC]] \|year=1989 \|title=Phase determination by multiple-wavelength X-ray diffraction: crystal structure of a basic blue copper protein from cucumbers \|journal=Science \|volume=241 \|pages=806–811 \|pmid=3406739 \|doi=10.1126/science.3406739 \|issue=4867 \|bibcode=1988Sci...241..806G}}

	~~==External links==~~
	*[http://skuld.bmsc.washington.edu/scatter/MAD_1.html MAD phasing] — an in depth tutorial with examples, illustrations, and references.

	~~===Computer programs===~~
	*[http://www-ssrl.slac.stanford.edu/absorb.html The SSRL Absorption Package] — {{cite journal \|author=Brennan S, Cowan PL \|year=1992 \|title=A suite of programs for calculating x-ray absorption, reflection and diffraction performance for a variety of materials at arbitrary wavelengths \|journal=Rev. Sci. Instrum. \|volume=63 \|page=850 \|doi=10.1063/1.1142625\|bibcode = 1992RScI...63..850B }}
	*[http://www.gwyndafevans.co.uk/chooch.html CHOOCH] — {{cite journal \|author=Evans G, Pettifer RF \|year=2001 \|title=CHOOCH: a program for deriving anomalous-scattering factors from X-ray fluorescence spectra \|journal=J. Appl. Cryst. \|volume=34 \|pages=82–86 \|doi=10.1107/S0021889800014655}}
	*[http://~~www.hwi.buffalo~~.~~edu~~/~~SnB~~/ ''Shake-and-Bake''] (''SnB'') — {{cite journal \|author=Smith GD, Nagar B, Rini JM, Hauptman HA, Blessing RH \|year=1998 \|title=The use of Snb to determine an anomalous scattering substructure \|journal=Acta Cryst D \|volume=54 \|pages=799–804 \|pmid=9757093 \|doi=10.~~1107/S0907444997018805 \|issue~~=~~Pt 5}}~~
	*[http://shelx.uni-ac.gwdg.de/SHELX/ SHELX] — {{cite book \|author=Sheldrick GM \|year=1998 \|chapter=SHELX: applications to macromolecules \|title=Direct methods for solving macromolecular structures \|editor=S Fortier \|pages=401–411 \|publisher=Dordrecht: Kluwer Academic Publishers \|isbn=0-7923-4949-0}}

	~~===Tutorials and examples===~~
	*{{cite web \|title=The method of Multiple wavelength Anomalous Diffraction using Synchrotron Radiation at optimal X-ray energies: Application to Protein Crystallography \|first=Gwyndaf \|last=Evans \|work=PhD Thesis \|date=October 1994 \|publisher=University of Warwick \|url=~~http://www.gwyndafevans.co.uk/thesis-html/thesis.html}}~~

	~~[[Category:Crystallography]~~]


	~~{{optics-stub}}~~

en>ArmbrustBot: /* References */re-categorisation per CFDS, replaced: Category:Potential → Category:Potentials using AWB

2013-10-09T14:13:24Z

References: re-categorisation per CFDS, replaced: Category:Potential → Category:Potentials using AWB

← Older revision		Revision as of 16:13, 9 October 2013
Line 1:		Line 1:
			'''Multiple isomorphous replacement''' or '''MIR''' is, historically speaking, the most common approach to solving the [[phase problem]] in [[X-ray crystallography]]. This method is conducted by soaking the crystal of a sample to be analyzed with a [[heavy atom]] solution or co-crystallization with the heavy atom. The addition of the heavy atom should not affect the crystal formation or [[unit cell]] dimensions in comparison to its native form, hence, they should be [[Isomorphism (crystallography)\|isomorphic]].

			Data sets from the native and heavy-atom derivative of the sample are first collected. Then the interpretation of the [[Patterson function\|Patterson difference map]] reveals the heavy atom's location in the unit cell. This allows both the [[amplitude]] and the [[Phase (waves)\|phase]] of the atom to be determined. Since the [[structure factor]] of the heavy atom derivative ('''F'''<sub>ph</sub>) of the crystal is the vector sum of the lone heavy atom ('''F'''<sub>h</sub>) and the native crystal ('''F'''<sub>p</sub>) then the phase of the native '''F'''<sub>p</sub> and '''F'''<sub>ph</sub> vectors can be solved geometrically.

	~~CMS provides the best platform to create websites that fulfill all the specifications~~ of ~~SEO. The next step is~~ to ~~visit your Word - Press blog dashboard~~. ~~These templates are professionally designed~~ and ~~are also Adsense ready. Word - Press also provides protection against spamming, as security is a measure issue. It's as simple as hiring a Wordpress plugin developer or learning how~~ to ~~create what is needed.~~ <br><br>~~Right starting from social media support~~ to ~~search engine optimization, such plugins are easily available within~~ the ~~Word - Press open source platform. If you loved this report~~ and ~~you would like to acquire extra details about~~ [~~http~~:~~//www~~.~~juegosdevestir~~.co.~~uk/profile/watfo wordpress dropbox backup] kindly stop by our own web-site~~. ~~After all~~, ~~Word - Press is free~~, ~~many of the enhancements for Word - Press like themes and plugins are also free~~, ~~and there is plenty of free information online about how to use Word - Press~~. ~~You are able to set them within your theme options and so they aid the search engine to get a suitable~~ title and ~~description for the~~ pages ~~that get indexed by Google~~. ~~Furthermore~~, ~~with the launch of Windows 7 Phone is the smart phone market nascent App~~. ~~This can be done by using a popular layout format and your unique Word~~ - ~~Press design can be achieved~~ in ~~other elements of the blog. <br><br>Just ensure that you hire experienced Word~~ - ~~Press CMS developer who is experienced enough to perform the task of Word~~ - ~~Press customization to get optimum benefits of Word~~ - ~~Press CMS~~. ~~But if you are not willing to choose cost to the detriment of quality~~, ~~originality and higher returns~~, ~~then go for a self~~-~~hosted wordpress blog and increase the presence~~ of ~~your business in this new digital age~~. ~~I hope this short Plugin Dynamo Review will assist you to differentiate whether Plugin Dynamo is Scam or a Genuine~~. ~~User friendly features~~ and ~~flexibility that Word~~ - ~~Press has to offer is second to none~~. ~~For any web design and development assignment~~, ~~this is definitely one~~ of ~~the key concerns~~, ~~specifically~~ for ~~online retail outlets as well as e-commerce websites~~. ~~<br><br>The next thing I did after installing Wordpress was to find myself~~ a ~~free good~~-~~looking Wordpress~~-~~theme offering the functionality I was after~~. ~~But the Joomla was created as the CMS over years of hard work~~. ~~To do this, you should link your posts to other relevant posts that you've created~~. ~~If you just want to share some picture and want to use it as a dairy, that you want to share with your friends and family members, then blogger would be an excellent choice~~. ~~Now all you have to do is log into your Word~~ - ~~Press site making use of the very same username~~ and ~~password that you initially had in your previous site. <br><br>Instead, you can easily just include it with our bodies integration field in e~~ - ~~Panel. I don~~'~~t want that for my visitors and I~~'~~m quite sure they don~~'~~t either. You can select color of your choice~~, ~~graphics of your favorite~~, ~~skins~~, ~~photos~~, pages~~, etc~~. ~~Change the entire appearance of you blog using themes with one click~~. As for ~~performing online business, websites~~ and ~~blogs are the only medium that are available~~ to ~~interact with customers and Word - Press perform this~~ work ~~with the help~~ of ~~cross~~-~~blog communication tools, comments and full user registration plug~~-~~ins.~~		:<math>\mathbf F_{ph} = \mathbf F_p + \mathbf F_h</math>

			At least two isomorphous derivatives must be evaluated since using only one will give two possible phases.

			==Examples==
			Some examples of heavy atoms used in protein MIR:
			*[[Mercury (element)\|Hg]]<sup>2+</sup> ions bind to [[thiol]] groups.
			*[[Uranyl]] salts ([[Uranium dioxide\|UO<sub>2</sub>]] + [[Nitrate\|NO<sub>3</sub>]]) bind between [[carboxyl]] groups in [[Aspartic acid\|Asp]] and [[Glutamic acid\|Glu]]
			*[[Lead\|Pb]] bind to [[Cysteine\|Cys]]
			*[[Platinum(IV) chloride\|PtCl<sub>4</sub><sup>2-</sup>]] ([[ion]]) bind to [[Histidine\|His]]

			== See also ==
			=== Anomalous Dispersion ===
			* [[Multi-wavelength anomalous dispersion]] (MAD)
			* [[Single wavelength anomalous dispersion]] (SAD)

			=== Isomorphous Replacement ===
			Two methods for providing the needed phasing information by introducing heavy atoms into isomorphous crystals:
			* Multiple isomorphous replacement (MIR); and
			* [[Single isomorphous replacement with anomalous signal]] (SIRAS)

			===Other===
			*[[Patterson map]]

			== References ==
			{{reflist}}

			===Further reading===
			*{{cite journal \|author=Hendrickson WA \|year=1985 \|title=Analysis of Protein Structure from Diffraction Measurement at Multiple Wavelengths \|journal=Trans. ACA \|volume=21}}
			*{{cite journal \|author=Karle J \|year=1980 \|title=Some Developments in Anomalous Dispersion for the Structural Investigation of Macromolecular Systems in Biology \|journal=International Journal of Quantum Chemistry: Quantum Biology Symposium \|volume=7 \|pages=357–367}}
			*{{cite journal \|author=Karle J \|year=1989 \|title=Linear Algebraic Analyses of Structures with One Predominant Type of Anomalous Scatterer \|journal=Acta Cryst. \|volume=A45 \|pages=303–307}}
			*{{cite journal \|author=Pahler A, Smith JL, Hendrickson WA \|year=1990 \|title=A Probability Representation for Phase Information from Multiwavelength Anomalous Dispersion \|journal=Acta Cryst. \|volume=A46 \|pages=537–540}}
			*{{cite journal \|author=Terwilliger TC \|year=1994 \|title=MAD Phasing: Bayesian Estimates of FA \|journal=Acta Cryst. \|volume=D50 \|pages=11–16}}
			*{{cite journal \|author=Terwilliger TC \|year=1994 \|title=MAD Phasing: Treatment of Dispersive Differences as Isomorphous Replacement Information \|journal=Acta Cryst. \|volume=D50 \|pages=17–23}}
			*{{cite journal \|author=Fourme R, Shepard W, Kahn R, l'Hermite G, de La Sierra IL \|year=1995 \|title=The Multiwavelength Anomalous Solvent Contrast (MASC) Method in Macrocolecular Crystallography \|journal=J. Synchrotron Rad. \|volume=2 \|pages=36–48 \|doi=10.1107/S0909049594006680}}
			*{{cite journal \|author=de la Fortelle E, Bricogne G \|year=1997 \|title=Maximum-Likelihood Heavy-Atom Parameter Refinement for Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods \|journal=Methods in Enzymology \|volume=276 \|pages=472–494 \|doi=10.1016/S0076-6879(97)76073-7 \|series=Methods in Enzymology \|isbn=978-0-12-182177-7}}
			*{{cite journal \|author=Hendrickson WA, Ogata CM \|year=1997 \|title=Phase Determination from Multiwavelength Anomalous Diffraction Measurements \|journal=Methods in Enzymology \|volume=276 \|pages=494–523 \|doi=10.1016/S0076-6879(97)76074-9 \|series=Methods in Enzymology \|isbn=978-0-12-182177-7}}
			*{{cite journal \|author=Bella J, Rossmann MG \|year=1998 \|title=A General Phasing Algorithm for Multiple MAD and MIR Data \|journal=Acta Cryst. \|volume=D54 \|pages=159–174}}
			*{{cite journal \|author=Guss JM, Merritt EA, Phizackerley RP, Hedman B, Murata M, [[Keith Hodgson\|Hodgson KO]], [[Hans Freeman\|Freeman HC]] \|year=1989 \|title=Phase determination by multiple-wavelength X-ray diffraction: crystal structure of a basic blue copper protein from cucumbers \|journal=Science \|volume=241 \|pages=806–811 \|pmid=3406739 \|doi=10.1126/science.3406739 \|issue=4867 \|bibcode=1988Sci...241..806G}}

			==External links==
			*[http://skuld.bmsc.washington.edu/scatter/MAD_1.html MAD phasing] — an in depth tutorial with examples, illustrations, and references.

			===Computer programs===
			*[http://www-ssrl.slac.stanford.edu/absorb.html The SSRL Absorption Package] — {{cite journal \|author=Brennan S, Cowan PL \|year=1992 \|title=A suite of programs for calculating x-ray absorption, reflection and diffraction performance for a variety of materials at arbitrary wavelengths \|journal=Rev. Sci. Instrum. \|volume=63 \|page=850 \|doi=10.1063/1.1142625\|bibcode = 1992RScI...63..850B }}
			*[http://www.gwyndafevans.co.uk/chooch.html CHOOCH] — {{cite journal \|author=Evans G, Pettifer RF \|year=2001 \|title=CHOOCH: a program for deriving anomalous-scattering factors from X-ray fluorescence spectra \|journal=J. Appl. Cryst. \|volume=34 \|pages=82–86 \|doi=10.1107/S0021889800014655}}
			*[http://www.hwi.buffalo.edu/SnB/ ''Shake-and-Bake''] (''SnB'') — {{cite journal \|author=Smith GD, Nagar B, Rini JM, Hauptman HA, Blessing RH \|year=1998 \|title=The use of Snb to determine an anomalous scattering substructure \|journal=Acta Cryst D \|volume=54 \|pages=799–804 \|pmid=9757093 \|doi=10.1107/S0907444997018805 \|issue=Pt 5}}
			*[http://shelx.uni-ac.gwdg.de/SHELX/ SHELX] — {{cite book \|author=Sheldrick GM \|year=1998 \|chapter=SHELX: applications to macromolecules \|title=Direct methods for solving macromolecular structures \|editor=S Fortier \|pages=401–411 \|publisher=Dordrecht: Kluwer Academic Publishers \|isbn=0-7923-4949-0}}

			===Tutorials and examples===
			*{{cite web \|title=The method of Multiple wavelength Anomalous Diffraction using Synchrotron Radiation at optimal X-ray energies: Application to Protein Crystallography \|first=Gwyndaf \|last=Evans \|work=PhD Thesis \|date=October 1994 \|publisher=University of Warwick \|url=http://www.gwyndafevans.co.uk/thesis-html/thesis.html}}

			[[Category:Crystallography]]


			{{optics-stub}}

en>Stan J Klimas: /* Determination */ +link

2012-05-27T12:21:11Z

Determination: +link

New page

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