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wwPDB X-ray validation report user guide

Full wwPDB X#0183;The wwPDB X-ray validation reports are prepared according to the recommendations of the wwPDB X-ray Validation Task Force (VTF) (Read et al.,2011).The report summarises the quality of the structure and highlights specific concerns by considering the atomic model,the diffraction data and the fit between the atomic model and the diffraction data (Gore et al.,2012).wwPDB 2014 NewswwPDB Worldwide Protein Data Bank.08/01/2014.wwPDB Events at IUCr (August 5-12) Meet wwPDB members from around the globe at the 23rd General Assembly and Congress of the International Union of Crystallography (IUCr,August 5-12,2014) in Montreal,Quebec,Canada.wwPDB 2013 News11/27/2013.New wwPDB service allows crystallographers to validate their own structures.The Worldwide Protein Data Bank (wwPDB) partners are pleased to announce that X-ray structure validation reports can now be generated on demand by macromolecular crystallographers by using the new stand-alone wwPDB validation server..The reports can be used to assess the quality of early,intermediate

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As a member of the wwPDB,the RCSB PDB curates and annotates PDB data according to agreed upon standards.The RCSB PDB also provides a variety of tools and resources.Users can perform simple and advanced searches based on annotations relating to sequence,structure and function.These molecules are visualized,downloaded,and analyzed by users who range from students to specialized scientists.RCSB PDB - 6O7F Mycobacterium tuberculosis L-alanine As a member of the wwPDB,the RCSB PDB curates and annotates PDB data according to agreed upon standards.The RCSB PDB also provides a variety of tools and resources.Users can perform simple and advanced searches based on annotations relating to sequence,structure and function.These molecules are visualized,downloaded,and analyzed by users who range from students to specialized scientists.

RCSB PDB - 6LHZ Structure of aerolysin-like protein

As a member of the wwPDB,the RCSB PDB curates and annotates PDB data according to agreed upon standards.The RCSB PDB also provides a variety of tools and resources.Users can perform simple and advanced searches based on annotations relating to sequence,structure and function.These molecules are visualized,downloaded,and analyzed by users who range from students to specialized scientists.Previous123456NextwwPDB X-ray validation report user guide Full wwPDB X#0183;The wwPDB X-ray validation reports are prepared according to the recommendations of the wwPDB X-ray Validation Task Force (VTF) (Read et al.,2011).The report summarises the quality of the structure and highlights specific concerns by considering the atomic model,the diffraction data and the fit between the atomic model and the diffraction data (Gore et al.,2012).Preliminary Full wwPDB X-ray Structure ValidationPreliminary Full wwPDB X-ray Structure Validation Report O i ebF 14,2020 04:25 PM GMT Deposition ID D_1292106756 This is a Preliminary ullF wwPDB X-ray Structure alidationV Report.This report is produced by the wwPDB Deposition System during initial

Preliminary Full wwPDB X-ray Structure Validation

Preliminary Full wwPDB X-ray Structure Validation Report O i ebF 14,2020 04:25 PM GMT Deposition ID D_1292106756 This is a Preliminary ullF wwPDB X-ray Structure alidationV Report.This report is produced by the wwPDB Deposition System during initialPreliminary Full wwPDB X-ray Structure ValidationPreliminary Full wwPDB X-ray Structure Validation Report O i Oct 1,2018 01:45 PM EDT Deposition ID D_1000235024 PDB ID (not yet assigned) This is a Preliminary ullF wwPDB X-ray Structure alidationV Report.This report is produced by the wwPDB Deposition System during initial deposition but before annotation of the structure.Preliminary Full wwPDB X-ray Structure ValidationPreliminary Full wwPDB X-ray Structure Validation Report O i May 31,2019 01:51 pm BST Deposition ID D_1292102609 PDB ID (not yet assigned) This is a Preliminary ullF wwPDB X-ray Structure alidationV Report.This report is produced by the wwPDB Deposition System during initial deposition but before annotation of the structure.

Full wwPDB X-ray Structure Validation Report i

Renementprogram X-PLOR Depositor R,R free 0.196 ,(Notavailable) 0.194 ,(Notavailable) Depositor DCC R free testset Notestagspresent.wwPDB-VP WilsonB-factor( Full wwPDB X#197;2) 29.3 Xtriage Anisotropy 0.406 Xtriage Bulksolventk sol(e/ Full wwPDB X#197;3),B sol( Full wwPDB X#197;2) 0.33,171.7 EDS L-testfortwinning1 Full wwPDB Xlt;jLj Full wwPDB Xgt;=0.46, Full wwPDB Xlt;L2 Full wwPDB Xgt;=0.28 Xtriage Estimatedtwinningfraction Full wwPDB X-ray Structure Validation Report iRenementprogram X-PLOR Depositor R,R free 0.196 ,(Notavailable) 0.194 ,(Notavailable) Depositor DCC R free testset Notestagspresent.wwPDB-VP WilsonB-factor( Full wwPDB X#197;2) 29.3 Xtriage Anisotropy 0.406 Xtriage Bulksolventk sol(e/ Full wwPDB X#197;3),B sol( Full wwPDB X#197;2) 0.33,171.7 EDS L-testfortwinning1 Full wwPDB Xlt;jLj Full wwPDB Xgt;=0.46, Full wwPDB Xlt;L2 Full wwPDB Xgt;=0.28 Xtriage Estimatedtwinningfraction Full wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report i Sep13,201806:56AMEDT PDBID 4X5F Title ecDHFRcomplexedwithfolateandNADP+at0.1MPa Authors Yamada,H.;Watanabe,N

Full wwPDB X-ray Structure Validation Report i

Full wwPDB X-ray Structure Validation Report i Sep13,201806:56AMEDT PDBID 4X5F Title ecDHFRcomplexedwithfolateandNADP+at0.1MPa Authors Yamada,H.;Watanabe,N Full wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report i Oct2,201910:24AMJST PDBID 6KUZ Title E.colibeta-galactosidase(E537Q)incomplexwithuorescentprobeKSL01Full wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report i Oct2,201910:24AMJST PDBID 6KUZ Title E.colibeta-galactosidase(E537Q)incomplexwithuorescentprobeKSL01

Full wwPDB X-ray Structure Validation Report i

Full wwPDB X-ray Structure Validation Report i Jun18,201807:45PMEDT PDBID 4F5S Title CrystalStructureofBovineSerumAlbumin Authors Bujacz,A.;Bujacz,G.Full wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report i Jul5,202006:31PMEDT PDBID 2AJF Title StructureofSARScoronavirusspikereceptor-bindingdomaincomplexedwithFull wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report i Jul22,202012:15PMEDT PDBID 6LU7 Title ThecrystalstructureofCOVID-19mainproteaseincomplexwithaninhibitor

Full wwPDB X-ray Structure Validation Report i

Full wwPDB X-ray Structure Validation Report i Jul10,202005:20PMEDT PDBID 6M36 Title The crystal structure of B.subtilis RsbV/RsbW complex in the monoclinicFull wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report i Feb18,201807:35pmGMT PDBID 3ERT Title HUMAN ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAINFull wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report i Feb18,201807:35pmGMT PDBID 3ERT Title HUMAN ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN

Full wwPDB X-ray Structure Validation Report i

Full wwPDB X-ray Structure Validation Report i Feb16,201805:27pmGMT PDBID 1ALC Title REFINED STRUCTURE OF BABOON ALPHA-LACTALBUMIN AT 1.7 ANGSTROMS RESOLUTION.Full wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report i Feb16,201805:27pmGMT PDBID 1ALC Title REFINED STRUCTURE OF BABOON ALPHA-LACTALBUMIN AT 1.7 ANGSTROMS RESOLUTION.Full wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report i Apr8,202009:51AMEDT PDBID 6M2N Title SARS-CoV-23CLprotease(3CLpro)incomplexwithanovelinhibitor

Full wwPDB X-ray Structure Validation Report i

Full wwPDB X-ray Structure Validation Report all X-ray entries and entries of similar resolution.The OWAB column contains the minimum,median,95th percentile and maximum values of the occupancy-weighted average B-factor per residue.The column labelled Q Full wwPDB Xlt;0:9 lists the number of (and percentage) of residues with anFull wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report all X-ray entries and entries of similar resolution.The OWAB column contains the minimum,median,95th percentile and maximum values of the occupancy-weighted average B-factor per residue.The column labelled Q Full wwPDB Xlt;0:9 lists the number of (and percentage) of residues with anFull wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report Totalnumberofatoms 4848 wwPDB-VP AverageB,allatoms

Full wwPDB X-ray Structure Validation Report i

Full wwPDB X-ray Structure Validation Report AverageB,allatoms( Full wwPDB X#197;2) 61.0 wwPDB-VP Xtriages analysis on translational NCS is as follows The largest o-origin peak in the Patter-son function is 11.46% of the height of the origin peak.No signicant pseudotranslation is de-Full wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report AverageB,allatoms( Full wwPDB X#197;2) 61.0 wwPDB-VP Xtriages analysis on translational NCS is as follows The largest o-origin peak in the Patter-son function is 11.46% of the height of the origin peak.No signicant pseudotranslation is de-Full wwPDB X-ray Structure Validation Report iFull wwPDB X-ray Structure Validation Report AverageB,allatoms( Full wwPDB X#197;2) 14.0 wwPDB-VP Xtriages analysis on translational NCS is as follows The largest o-origin peak in the Patter-son function is 10.50% of the height of the origin peak.No signicant pseudotranslation is de-

Full wwPDB X-ray Structure Validation Report O i

Page 3 uFll wwPDB X-ray Structure alidationV Report 3CP7 2 Entry composition O i There are 3 unique types of molecules in this entry.The entry contains 3871 atoms,of which 0 are hydrogens and 0 are deuteriums.In the tables below,the ZeroOcc column contains theFull wwPDB X-ray Structure Validation Report O iPage 2 Full wwPDB X-ray Structure Validation Report 2WY0 1 Overall quality at a glance O i The reported resolution of this entry is 2.38 A.Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic.The table shows the number of entries on which the scores are based.Metric Whole archiveFull wwPDB X-ray Structure Validation Report O iPage 2 Full wwPDB X-ray Structure Validation Report 1BLL 1 Overall quality at a glance O i The reported resolution of this entry is 2.40 A.Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic.The table shows the number of entries on which the scores are based.Metric Whole archive

12345NextwwPDB Validation Reports

The validation reports continue to be developed and improved as we receive recommendations from the expert Validation Task Forces (VTF) for X-ray,NMR,and EM,as we develop the wwPDB Deposition Annotation (DA) system,and as we collect feedback from depositors and users.

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