X-ray crystallography: Difference between revisions
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|Flow chart showing the major steps in X-ray protein crystallography. ([http://upload.wikimedia.org/wikipedia/commons/7/73/X_ray_diffraction.png Image] from Wikimedia courtesy Thomas Splettstoesser. | |Flow chart showing the major steps in X-ray protein crystallography. ([http://upload.wikimedia.org/wikipedia/commons/7/73/X_ray_diffraction.png Image] from Wikimedia courtesy Thomas Splettstoesser.) | ||
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About | About 88% of the models (entries) in the [[Protein Data Bank|World Wide Protein Data Bank]] were determined by X-ray crystallography (August, 2021). (About 7% were determined by [[NMR|solution nuclear magnetic resonance]], and about 5% by [[cryo-EM]].) Analysis of x-ray diffraction patterns from protein crystals produces an [[Electron density maps|electron density map]], into which an atomic model of the protein is fitted. Major errors sometimes occur when fitting models in to low-[[Resolution|resolution]] electron density maps (see [[Quality assessment for molecular models]]). The value of [[Free R]] is the best clue as to whether major errors may be present in a published model. | ||
Obtaining diffraction-quality crystals of proteins can be very difficult for some proteins, despite many recent advances<ref name="intro">PMID: 24419610</ref>. For every new protein sequence targeted for X-ray crystallography, about one in twenty is solved<ref>[https://www.umass.edu/molvis/workshop/allstruc/xrc_succ.htm Success Rates in Protein Crystallography]</ref><ref>[https://www.umass.edu/molvis/workshop/allstruc/xsuccess.htm Structural Genomics Progress Chart]</ref>. Efforts are underway to improve this success rate<ref>PMID: 22653729</ref>. | |||
<center><table width="450"><tr><td>[[Image:Protein crystals samatey.png]]</td><td> </td><td>Crystals of the [[Flagellar hook of bacteria|flagellar hook protein]] FlgE from ''C. jejuni'' produced in the [[Fadel_A._Samatey_Group|Samatey lab]].</td></tr></table></center> | |||
Publication of solved structures involves depositing an [[Atomic coordinate file|atomic coordinate file]] ([[PDB file]]) in the [[Protein Data Bank|World Wide Protein Data Bank]]. | |||
About two-thirds of published crystallographic models can be improved by automated re-refinement: see [[PDB REDO]]. | |||
==See Also== | ==See Also== | ||
*[http://www.pdb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/methods.html Methods for Determining Atomic Structures] | |||
*[[Electron density maps]] | |||
*[http://en.wikipedia.org/wiki/X-ray_crystallography X-ray Crystallography at Wikipedia] | |||
*[http://hamptonresearch.com/gallery.aspx Protein Crystal Gallery] | |||
*[[Crystal contacts]] | |||
*[[Biological Unit]] | |||
*[[Quality assessment for molecular models]] | |||
*[[Resolution]] | *[[Resolution]] | ||
*[[R value]] | *[[R value]] | ||
*[[Free R]] | *[[Free R]] | ||
*[[Hydrogen in macromolecular models]] | |||
*[[Water in macromolecular models]] | |||
*[[Highest impact structures]] of all time. | *[[Highest impact structures]] of all time. | ||
*[[Nobel Prizes for 3D Molecular Structure]] | |||
*[[NMR Ensembles of Models]] | |||
===DNA X-Ray Diffraction=== | |||
* Links to explanations of Rosalind Franklin's original DNA diffraction pattern, used by Watson and Crick, will be found in the '''See Also''' section of the article on [[DNA]]. | |||
==Further Reading== | |||
*[https://www.elsevier.com/books/crystallography-made-crystal-clear/rhodes/978-0-12-587073-3 Crystallography Made Crystal Clear: a guide for users of macromolecular models], a book by Gale Rhodes. | |||
*[http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction Introduction to PDB Data]. | |||
==Notes & References== | ==Notes & References== | ||
<references /> | <references /> | ||