X-ray crystallography - Revision history

http://52.214.119.220/wiki/index.php?action=history&feed=atom&title=X-ray_crystallography X-ray crystallography - Revision history 2026-04-05T00:38:30Z Revision history for this page on the wiki MediaWiki 1.11.2 http://52.214.119.220/wiki/index.php?title=X-ray_crystallography&diff=3631514&oldid=prev Eric Martz at 22:18, 15 September 2022 2022-09-15T22:18:59Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 22:18, 15 September 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 12:</td> <td colspan="2" class="diff-lineno">Line 12:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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]].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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]].</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>About two-thirds of published crystallographic models can be improved by automated re-refinement: see [[PDB REDO]].</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See Also==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See Also==</div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=X-ray_crystallography&diff=3631512&oldid=prev Eric Martz at 22:13, 15 September 2022 2022-09-15T22:13:36Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 22:13, 15 September 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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>[<del style="color: red; font-weight: bold; text-decoration: none;">http</del>://<del style="color: red; font-weight: bold; text-decoration: none;">proteinexplorer</del>.<del style="color: red; font-weight: bold; text-decoration: none;">org</del>/<del style="color: red; font-weight: bold; text-decoration: none;">gpsi</del>/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>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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>[<ins style="color: red; font-weight: bold; text-decoration: none;">https</ins>://<ins style="color: red; font-weight: bold; text-decoration: none;">www</ins>.<ins style="color: red; font-weight: bold; text-decoration: none;">umass.edu/molvis/workshop</ins>/<ins style="color: red; font-weight: bold; text-decoration: none;">allstruc</ins>/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>. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><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></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><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></div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=X-ray_crystallography&diff=3631511&oldid=prev Eric Martz at 22:09, 15 September 2022 2022-09-15T22:09:43Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 22:09, 15 September 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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>[http://proteinexplorer.org/gpsi/xrc_succ.htm Success Rates in Protein Crystallography]</ref><ref>[<del style="color: red; font-weight: bold; text-decoration: none;">http</del>://<del style="color: red; font-weight: bold; text-decoration: none;">proteinexplorer</del>.<del style="color: red; font-weight: bold; text-decoration: none;">org</del>/<del style="color: red; font-weight: bold; text-decoration: none;">gpsi</del>/xsuccess.htm Structural Genomics Progress Chart]</ref>. Efforts are underway to improve this success rate<ref>PMID: 22653729</ref>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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>[http://proteinexplorer.org/gpsi/xrc_succ.htm Success Rates in Protein Crystallography]</ref><ref>[<ins style="color: red; font-weight: bold; text-decoration: none;">https</ins>://<ins style="color: red; font-weight: bold; text-decoration: none;">www</ins>.<ins style="color: red; font-weight: bold; text-decoration: none;">umass.edu/molvis/workshop</ins>/<ins style="color: red; font-weight: bold; text-decoration: none;">allstruc</ins>/xsuccess.htm Structural Genomics Progress Chart]</ref>. Efforts are underway to improve this success rate<ref>PMID: 22653729</ref>. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><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></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><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></div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=X-ray_crystallography&diff=3631510&oldid=prev Eric Martz at 22:06, 15 September 2022 2022-09-15T22:06:02Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 22:06, 15 September 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Obtaining diffraction-quality crystals of proteins <del style="color: red; font-weight: bold; text-decoration: none;">remains </del>very difficult, 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>[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>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Obtaining diffraction-quality crystals of proteins <ins style="color: red; font-weight: bold; text-decoration: none;">can be </ins>very difficult <ins style="color: red; font-weight: bold; text-decoration: none;">for some proteins</ins>, 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>[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>. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><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></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><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></div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=X-ray_crystallography&diff=3437878&oldid=prev Eric Martz at 00:35, 12 August 2021 2021-08-12T00:35:04Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 00:35, 12 August 2021</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 2:</td> <td colspan="2" class="diff-lineno">Line 2:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|[[Image:X ray diffraction flow chart Splettstoesser.png|400px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|[[Image:X ray diffraction flow chart Splettstoesser.png|400px]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|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.<ins style="color: red; font-weight: bold; text-decoration: none;">)</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=X-ray_crystallography&diff=3437877&oldid=prev Eric Martz at 00:32, 12 August 2021 2021-08-12T00:32:32Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 00:32, 12 August 2021</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>About <del style="color: red; font-weight: bold; text-decoration: none;">85</del>% of the models (entries) in the [[Protein Data Bank|World Wide Protein Data Bank]] were determined by X-ray crystallography. (<del style="color: red; font-weight: bold; text-decoration: none;">Most of the remaining 15</del>% 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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>About <ins style="color: red; font-weight: bold; text-decoration: none;">88</ins>% of the models (entries) in the [[Protein Data Bank|World Wide Protein Data Bank]] were determined by X-ray crystallography <ins style="color: red; font-weight: bold; text-decoration: none;">(August, 2021)</ins>. (<ins style="color: red; font-weight: bold; text-decoration: none;">About 7</ins>% were determined by [[NMR|solution nuclear magnetic resonance<ins style="color: red; font-weight: bold; text-decoration: none;">]], and about 5% by [[cryo-EM</ins>]].) 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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Obtaining diffraction-quality crystals of proteins remains very difficult, 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>[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>. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Obtaining diffraction-quality crystals of proteins remains very difficult, 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>[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>. </div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=X-ray_crystallography&diff=3163145&oldid=prev Eric Martz at 17:34, 1 March 2020 2020-03-01T17:34:52Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:34, 1 March 2020</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>About 85% of the models (entries) in the [[Protein Data Bank|World Wide Protein Data Bank]] were determined by X-ray crystallography<del style="color: red; font-weight: bold; text-decoration: none;"><ref name="intro">PMID: 24419610</ref></del>. (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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Obtaining diffraction-quality crystals of proteins remains very difficult, despite many recent advances<ins style="color: red; font-weight: bold; text-decoration: none;"><ref name="intro">PMID: 24419610</ref></ins>. 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>. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><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></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><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></div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=X-ray_crystallography&diff=3163144&oldid=prev Eric Martz at 17:33, 1 March 2020 2020-03-01T17:33:55Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:33, 1 March 2020</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>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.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>About 85% of the models (entries) in the [[Protein Data Bank|World Wide Protein Data Bank]] were determined by X-ray crystallography<ins style="color: red; font-weight: bold; text-decoration: none;"><ref name="intro">PMID: 24419610</ref></ins>. (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.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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>. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>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>. </div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=X-ray_crystallography&diff=2882781&oldid=prev Eric Martz: /* Further Reading */ 2018-04-10T15:16:17Z

<p><span class="autocomment">Further Reading</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:16, 10 April 2018</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 42:</td> <td colspan="2" class="diff-lineno">Line 42:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[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.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*[<del style="color: red; font-weight: bold; text-decoration: none;">https</del>://<del style="color: red; font-weight: bold; text-decoration: none;">www</del>.rcsb.org/pdb/<del style="color: red; font-weight: bold; text-decoration: none;">static.do?p=general_information%5Cabout_pdb%5Cnature_of_3d_structural_data.html Nature of 3D Structural </del>Data].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*[<ins style="color: red; font-weight: bold; text-decoration: none;">http</ins>://<ins style="color: red; font-weight: bold; text-decoration: none;">pdb101</ins>.rcsb.org/<ins style="color: red; font-weight: bold; text-decoration: none;">learn/guide-to-understanding-</ins>pdb<ins style="color: red; font-weight: bold; text-decoration: none;">-data</ins>/<ins style="color: red; font-weight: bold; text-decoration: none;">introduction Introduction to PDB </ins>Data].</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Notes & References==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Notes & References==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><references /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><references /></div></td></tr> </table>

Eric Martz http://52.214.119.220/wiki/index.php?title=X-ray_crystallography&diff=2882744&oldid=prev Eric Martz: /* Further Reading */ 2018-04-09T21:38:25Z

<p><span class="autocomment">Further Reading</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 21:38, 9 April 2018</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 42:</td> <td colspan="2" class="diff-lineno">Line 42:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[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.</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*[https://www.rcsb.org/pdb/static.do?p=general_information%5Cabout_pdb%5Cnature_of_3d_structural_data.html Nature of 3D Structural Data].</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Notes & References==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Notes & References==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><references /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><references /></div></td></tr> </table>

Eric Martz