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5pel

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PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 114)

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 ==PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 114)==
-<StructureSection load='5pel' size='340' side='right' caption='[[5pel]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='5pel' size='340' side='right'caption='[[5pel]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5pel]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PEL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PEL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5pel]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PEL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BAZ2B, KIAA1476 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=5pel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pel OCA], [http://pdbe.org/5pel PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pel RCSB], [http://www.ebi.ac.uk/pdbsum/5pel PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pel 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=5pel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pel OCA], [https://pdbe.org/5pel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pel RCSB], [https://www.ebi.ac.uk/pdbsum/5pel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pel ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BAZ2B_HUMAN BAZ2B_HUMAN]] May play a role in transcriptional regulation interacting with ISWI.
+[https://www.uniprot.org/uniprot/BAZ2B_HUMAN BAZ2B_HUMAN] May play a role in transcriptional regulation interacting with ISWI.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches.
-A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.,Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F Nat Commun. 2017 Apr 24;8:15123. doi: 10.1038/ncomms15123. PMID:28436492<ref>PMID:28436492</ref>
+==See Also==
+*[[Bromodomain adjacent to zinc finger 3D structures|Bromodomain adjacent to zinc finger 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5pel" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Arrowsmith, C H]]
+[[Category: Large Structures]]
-[[Category: Bountra, C]]
+[[Category: Arrowsmith CH]]
-[[Category: Bradley, A R]]
+[[Category: Bountra C]]
-[[Category: Brandao-Neto, J]]
+[[Category: Bradley AR]]
-[[Category: Brennan, P E]]
+[[Category: Brandao-Neto J]]
-[[Category: Collins, P]]
+[[Category: Brennan PE]]
-[[Category: Cox, O]]
+[[Category: Collins P]]
-[[Category: Delft, F von]]
+[[Category: Cox O]]
-[[Category: Dias, A]]
+[[Category: Dias A]]
-[[Category: Douangamath, A]]
+[[Category: Douangamath A]]
-[[Category: Edwards, A]]
+[[Category: Edwards A]]
-[[Category: Fairhead, M]]
+[[Category: Fairhead M]]
-[[Category: Krojer, T]]
+[[Category: Krojer T]]
-[[Category: MacLean, E]]
+[[Category: MacLean E]]
-[[Category: Ng, J]]
+[[Category: Ng J]]
-[[Category: Pearce, N M]]
+[[Category: Pearce NM]]
-[[Category: Renjie, Z]]
+[[Category: Renjie Z]]
-[[Category: Sethi, R]]
+[[Category: Sethi R]]
-[[Category: Talon, R]]
+[[Category: Talon R]]
-[[Category: Vollmar, M]]
+[[Category: Vollmar M]]
-[[Category: Wright, N]]
+[[Category: Wright N]]
-[[Category: Bromodomain]]
+[[Category: Von Delft F]]
-[[Category: Dna binding protein]]
-[[Category: Epigenetic]]
-[[Category: Pandda]]
-[[Category: Sgc - diamond i04-1 fragment screening]]

5pel

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PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 114)

Structural highlights

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