X-ray crystallography: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, David Canner

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 |[[Image:X ray diffraction flow chart Splettstoesser.png|400px]]
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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.)
 |}
-About 85% of the models (entries) in the [[Protein Data Bank|World Wide Protein Data Bank]] were determined by X-ray crystallography. (Most of the remaining 15% were determined by [[NMR|solution nuclear magnetic resonance]].) 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.
+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 remains very difficult, despite many recent advances. For every new protein sequence targeted for X-ray crystallography, about one in twenty is solved<ref>[http://proteinexplorer.org/gpsi/xrc_succ.htm Success Rates in Protein Crystallography]</ref><ref>[http://proteinexplorer.org/gpsi/xsuccess.htm Structural Genomics Progress Chart]</ref>. Efforts are underway to improve this success rate<ref>PMID: 22653729</ref>.
+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>&nbsp;</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==
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 *[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.
-*[https://www.rcsb.org/pdb/static.do?p=general_information%5Cabout_pdb%5Cnature_of_3d_structural_data.html Nature of 3D Structural Data].
+*[http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction Introduction to PDB Data].
 ==Notes & References==
 <references />