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| | ==A revised partiality model and post-refinement algorithm for X-ray free-electron laser data== | | ==A revised partiality model and post-refinement algorithm for X-ray free-electron laser data== |
| - | <StructureSection load='4zqx' size='340' side='right' caption='[[4zqx]], [[Resolution|resolution]] 1.46Å' scene=''> | + | <StructureSection load='4zqx' size='340' side='right'caption='[[4zqx]], [[Resolution|resolution]] 1.46Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4zqx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Uranotaenia_sapphirina_cypovirus Uranotaenia sapphirina cypovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZQX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4zqx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Uranotaenia_sapphirina_cypovirus Uranotaenia sapphirina cypovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZQX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.46Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4s1l|4s1l]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4zqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zqx OCA], [http://pdbe.org/4zqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zqx RCSB], [http://www.ebi.ac.uk/pdbsum/4zqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zqx ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4zqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zqx OCA], [https://pdbe.org/4zqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zqx RCSB], [https://www.ebi.ac.uk/pdbsum/4zqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zqx ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q5EK29_9REOV Q5EK29_9REOV] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4zqx" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4zqx" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Polyhedrin|Polyhedrin]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Uranotaenia sapphirina cypovirus]] | | [[Category: Uranotaenia sapphirina cypovirus]] |
| - | [[Category: Brewster, A S]] | + | [[Category: Brewster AS]] |
| - | [[Category: Evans, G]] | + | [[Category: Evans G]] |
| - | [[Category: Ginn, H M]] | + | [[Category: Ginn HM]] |
| - | [[Category: Grimes, J]] | + | [[Category: Grimes J]] |
| - | [[Category: Hattne, J]] | + | [[Category: Hattne J]] |
| - | [[Category: Sauter, N K]] | + | [[Category: Sauter NK]] |
| - | [[Category: Stuart, D I]] | + | [[Category: Stuart DI]] |
| - | [[Category: Sutton, G]] | + | [[Category: Sutton G]] |
| - | [[Category: Wagner, A]] | + | [[Category: Wagner A]] |
| - | [[Category: Free-electron laser]]
| + | |
| - | [[Category: Partiality]]
| + | |
| - | [[Category: Post-refinement]]
| + | |
| - | [[Category: Viral protein]]
| + | |
| Structural highlights
Function
Q5EK29_9REOV
Publication Abstract from PubMed
Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 A wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definition of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating the Rsplit value) of 3.15% to 1.46 A resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 A wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.
A revised partiality model and post-refinement algorithm for X-ray free-electron laser data.,Ginn HM, Brewster AS, Hattne J, Evans G, Wagner A, Grimes JM, Sauter NK, Sutton G, Stuart DI Acta Crystallogr D Biol Crystallogr. 2015 Jun;71(Pt 6):1400-10. doi:, 10.1107/S1399004715006902. Epub 2015 May 23. PMID:26057680[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ginn HM, Brewster AS, Hattne J, Evans G, Wagner A, Grimes JM, Sauter NK, Sutton G, Stuart DI. A revised partiality model and post-refinement algorithm for X-ray free-electron laser data. Acta Crystallogr D Biol Crystallogr. 2015 Jun;71(Pt 6):1400-10. doi:, 10.1107/S1399004715006902. Epub 2015 May 23. PMID:26057680 doi:http://dx.doi.org/10.1107/S1399004715006902
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