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]]. | ||