X-ray crystallography: Difference between revisions
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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 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. | ||
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>. | 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>. | ||
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]]. | 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]]. | ||
Revision as of 19:40, 30 July 2012
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| Flow chart showing the major steps in X-ray protein crystallography. (Image from Wikimedia courtesy Thomas Splettstoesser. |
About 85% of the models (entries) in the World Wide Protein Data Bank were determined by X-ray crystallography. (Most of the remaining 15% were determined by solution nuclear magnetic resonance.) Analysis of x-ray diffraction patterns from protein crystals produces an electron density map, into which an atomic model of the protein is fitted. Major errors sometimes occur when fitting models in to low-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[1][2]. Efforts are underway to improve this success rate[3].
Publication of solved structures involves depositing an atomic coordinate file (PDB file) in the World Wide Protein Data Bank.
See AlsoSee Also
- Methods for Determining Atomic Structures
- X-ray Crystallography at Wikipedia
- Protein Crystal Gallery
- Crystal contacts
- Biological Unit
Further ReadingFurther Reading
- Crystallography Made Crystal Clear: a guide for users of macromolecular models, a book by Gale Rhodes.
Notes & ReferencesNotes & References
- ↑ Success Rates in Protein Crystallography
- ↑ Structural Genomics Progress Chart
- ↑ Boutet S, Lomb L, Williams GJ, Barends TR, Aquila A, Doak RB, Weierstall U, Deponte DP, Steinbrener J, Shoeman RL, Messerschmidt M, Barty A, White TA, Kassemeyer S, Kirian RA, Seibert MM, Montanez PA, Kenney C, Herbst R, Hart P, Pines J, Haller G, Gruner SM, Philipp HT, Tate MW, Hromalik M, Koerner LJ, van Bakel N, Morse J, Ghonsalves W, Arnlund D, Bogan MJ, Caleman C, Fromme R, Hampton CY, Hunter MS, Johansson L, Katona G, Kupitz C, Liang M, Martin AV, Nass K, Redecke L, Stellato F, Timneanu N, Wang D, Zatsepin NA, Schafer D, Defever J, Neutze R, Fromme P, Spence JC, Chapman HN, Schlichting I. High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography. Science. 2012 May 31. PMID:22653729 doi:10.1126/science.1217737