wwPDB: Validation Reports

<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="description" content="wwPDB: Worldwide Protein Data Bank"> <meta name="author" content="wwPDB.org"> <link rel="shortcut icon" href="/favicon.ico"> <link href="/css/bootstrap-v3.1.1.min.css" rel="stylesheet"> <link href="/tools/font-awesome-4.4.0/css/font-awesome.min.css" rel="stylesheet"> <link href="/css/wwPDB.css?v=4" rel="stylesheet"> <link href='https://fonts.googleapis.com/css?family=Exo+2:600' rel='stylesheet' type='text/css'> <link href='https://fonts.googleapis.com/css?family=Roboto:300, 400,500,700' rel='stylesheet' type='text/css'> <link href='https://fonts.googleapis.com/css?family=Petit+Formal+Script' rel='stylesheet' type='text/css'>  <script async src="https://www.googletagmanager.com/gtag/js?id=G-5ED0CQCXV6"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new 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class='active'><a href='/validation/validation-reports' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Validation Reports</a></li> <li ><a href='/validation/validation-servers' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Validation Servers</a></li> <li ><a href='/validation/onedep-validation-web-service-interface' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> OneDep Validation API</a></li> </ul> </div> <div class="col-md-9"> <div class="wwpdb-content">  <style> div.hdlist { margin: 20px 0; } div.hdlist table tr { vertical-align:top; } div.hdlist table tr td.hdlist1, div.hdlist table tr td.hdlist2 { padding: 4px; } div.hdlist table tr td.hdlist1 { font-weight:bold; } #toctitle{color:#669966;font-size: 14px;} div.admonitionblock table td.content{padding-left:1.125em;padding-right:1.25em;border-left:1px solid #ddddd8;color:rgba(0,0,0,.6)} </style> <div id="header"> </div> <div id="content"> <div class="sect1"> <a class="anchor" id="_wwpdb_validation_reports"></a> <h2>wwPDB Validation Reports</h2> <div class="sectionbody"> <div class="paragraph"> <p>The wwPDB provides depositors with detailed reports (PDF and XML files) that include the results of model and experimental data validation, as part of the curation of all entries.</p> </div> <div class="paragraph"> <p>As these wwPDB validation reports provide an assessment of structure quality using widely accepted standards and criteria, the wwPDB partners strongly encourage journal editors and referees to request them from authors as part of the manuscript submission and review process. The reports are date-stamped and display the logo of the wwPDB site where the entry was curated. They contain the same information, regardless of which wwPDB site processed the entry. Provision of wwPDB validation reports is already required by <em>eLife, The Journal of Biological Chemistry</em>, and the International Union of Crystallography (IUCr) journals as part of their manuscript-submission process.</p> </div> <div class="paragraph"> <p>The validation reports continue to be developed and improved as we receive recommendations from the expert Validation Task Forces (VTF) for <a href="/task/xray">X-ray</a>, <a href="/task/nmr">NMR</a>, and <a href="/task/em">EM</a>, as we develop the <a href="/deposition/system-information">wwPDB Deposition & Annotation (D&A) system</a>, and as we collect feedback from depositors and users.</p> </div> <div class="paragraph"> <p>The validation reports for all structures deposited in the PDB archive have been updated in September 2020 with 2019 statistics (<a href="https://www.wwpdb.org/news/news?year=2020#5f6377df07302466657ec0df">announcement</a>).</p> </div> <div class="paragraph"> <p>Validation reports for all Nuclear Magnetic Resonance (NMR) and 3D Cryo Electron Microscopy (3DEM) structures already represented in the global PDB archive were made publicly available in May 2016 (<a href="/news/news?year=2016#03-May-2016">announcement</a>).</p> </div> <div class="sect2"> <a class="anchor" id="links"></a> <h3>Useful resources and links</h3> <div class="ulist"> <ul> <li> <p>Validation Report User Guides for <a href="./2017/XrayValidationReportHelp">X-ray</a>, <a href="./2017/NMRValidationReportHelp">NMR</a>, <a href="./2017/EMValidationReportHelp">EM model</a>, <a href="./2017/EMMapValidationReportHelp">EM map only</a>, <a href="./2017/EMTomogramValidationReportHelp">EM tomogram</a>.</p> </li> <li> <p>Validation Report <a href="./2017/FAQs">FAQs</a>.</p> </li> <li> <p>Validation Report <a href="/news/news.php?item=02-August-2013">announcement</a></p> </li> <li> <p>Sample validation report PDFs for:</p> <div class="ulist"> <ul> <li> <p><a href="./samples/1cbs/1cbs_validation.pdf" target="_blank" rel="noopener">1CBS</a>, a 1.8Å resolution X-ray structure of a small protein and a ligand, an entry with better overall quality relative to all X-ray structures.</p> </li> <li> <p><a href="./samples/1fcc/1fcc_validation.pdf" target="_blank" rel="noopener">1FCC</a>, a 3.2Å resolution structure with worse overall quality relative to all X-ray structures.</p> </li> <li> <p><a href="./samples/1eg1/1eg1_validation.pdf" target="_blank" rel="noopener">1EG1</a>, a 3.6Å resolution structure with possible ligand geometry and fit to density issues.</p> </li> <li> <p><a href="./samples/7jia/7jia_validation.pdf" target="_blank" rel="noopener">7JIA</a>, a solution NMR entry with restraints analysis.</p> </li> <li> <p><a href="./samples/6qwr/6qwr_validation.pdf" target="_blank" rel="noopener">6QWR</a>, a solid-state NMR entry.</p> </li> <li> <p><a href="./samples/EMD_4960/emd_4960_validation.pdf" target="_blank" rel="noopener">EMD-4960</a>, a 3.9Å resolution EM map including ligand, FSC curve and half-maps.</p> </li> <li> <p><a href="./samples/EMD_21212/emd_21212_6vja_validation.pdf" target="_blank" rel="noopener">EMD-21212/6VJA</a>, a 3.30Å single particle EM reconstruction with model including FSC curve, half-maps and mask.</p> </li> <li> <p><a href="./samples/EMD_0509/emd_0509_validation.pdf" target="_blank" rel="noopener">EMD-0509</a>, analysis of an EM tomogram.</p> </li> </ul> </div> </li> <li> <p>Validation information and reports for released PDB entries are available from the entry pages at <a href="https://pdbj.org/" target="_blank" rel="noopener">PDBj</a>, <a href="https://www.rcsb.org/" target="_blank" rel="noopener">RCSB PDB</a> and <a href="https://pdbe.org/" target="_blank" rel="noopener">PDBe</a>.</p> </li> <li> <p>FTP/HTTP access to validation reports, in PDF and XML format, for all released entries from <a href="https://files.wwpdb.org/pub/pdb/validation_reports/" target="_blank" rel="noopener">wwPDB</a>, <a href="https://files.rcsb.org/pub/pdb/validation_reports/" target="_blank" rel="noopener">RCSB PDB</a>, <a href="ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/" target="_blank" rel="noopener">PDBe</a> or <a href="ftp://ftp.pdbj.org/pub/pdb/validation_reports/" target="_blank" rel="noopener">PDBj</a>.</p> </li> <li> <p>Validation XML Schema: <a href="./schema/wwpdb_validation_v1.xsd" target="_blank" rel="noopener">v1</a>, <a href="./schema/wwpdb_validation_v002.xsd" target="_blank" rel="noopener">v002</a>, <a href="./schema/wwpdb_validation_v003.xsd" target="_blank" rel="noopener">v003</a>, <a href="./schema/wwpdb_validation_v004.xsd" target="_blank" rel="noopener">v004</a>. <a href="./schema/wwpdb_validation_v005.xsd" target="_blank" rel="noopener">v005</a>. <a href="./schema/wwpdb_validation_v5.01.xsd" target="_blank" rel="noopener">v5.01</a>. <a href="./schema/wwpdb_validation_v6.00.xsd" target="_blank" rel="noopener">v6.00</a>. <a href="./schema/wwpdb_validation_v6.01.xsd" target="_blank" rel="noopener">v6.01</a>. <a href="./schema/wwpdb_validation_v6.02.xsd" target="_blank" rel="noopener">v6.02</a>. <a href="./schema/wwpdb_validation_v6.03.xsd" target="_blank" rel="noopener">v6.03</a>. <a href="./schema/wwpdb_validation_v6.04.xsd" target="_blank" rel="noopener">v6.04</a>.</p> </li> <li> <p>Information on <a href="/validation/validation-servers">Stand-alone wwPDB validation servers</a> that allow experimental structural biologists to produce reports and validate their models prior to publication and deposition.</p> </li> <li> <p><a href="http://deposit.wwpdb.org/deposition/" target="_blank" rel="noopener">wwPDB Deposition System</a></p> </li> </ul> </div> <div class="paragraph"> <p>Please send any comments, questions or suggestions on the reports to <a href="mailto:validation@mail.wwpdb.org">validation@mail.wwpdb.org</a></p> </div> </div> </div> </div> </div>  </div> </div> </div> <br> <footer class="footer"> <div class="container-fluid hidden-print" 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wwPDB: Validation Reports