June 13, 2018 Dataset Open Access

Krojer, Tobias

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  <identifier identifierType="DOI">10.5281/zenodo.1244111</identifier>
  <creators>
    <creator>
      <creatorName>Krojer, Tobias</creatorName>
      <givenName>Tobias</givenName>
      <familyName>Krojer</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-0661-0814</nameIdentifier>
      <affiliation>Structural Genomics Consortium</affiliation>
    </creator>
  </creators>
  <titles>
    <title>PanDDA analysis of NUDT7 screened against DSPL and OxXChem fragment libraries</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <subjects>
    <subject>PanDDA</subject>
    <subject>Crystallographic Fragment Screening</subject>
    <subject>Diamond Light Source beamline I04-1</subject>
    <subject>XChem</subject>
    <subject>Structural Genomics Consortium</subject>
    <subject>Fragment Based Lead Discovery</subject>
    <subject>NUDIX domain</subject>
    <subject>NUDT7</subject>
    <subject>Target Enabling Package (TEP)</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2018-06-13</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1244111</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1244110</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;&lt;a href="https://www.thesgc.org/scientists/groups/oxford"&gt;SGC Oxford&lt;/a&gt; has performed a crystallographic fragment screen on the human peroxisomal coenzyme A diphosphatase NUDT7 (&lt;a href="http://www.uniprot.org/uniprot/P0C024"&gt;UniProtKB - P0C024&lt;/a&gt;). All structures with clearly identifiable ligands were deposited in the &lt;a href="http://www.wwpdb.org/"&gt;Protein Data Bank&lt;/a&gt; under Group Deposition ID G_1002045. The final structures and the relevant PanDDA event maps can be found at the &lt;a href="https://www.thesgc.org/fragment-screening"&gt;SGC fragment screening website&lt;/a&gt;. This work is part of the &lt;a href="https://www.thesgc.org/tep"&gt;Target Enabling Package (TEP)&lt;/a&gt; program at SGC and the complete TEP for NUDT7 is will also be available on ZENODO shortly.&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&lt;strong&gt;Experiment&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;Crystals were prepared at the &lt;a href="http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html"&gt;XChem &lt;/a&gt;facility of the &lt;a href="http://www.diamond.ac.uk"&gt;Diamond Light Source&lt;/a&gt; (DLS). Briefly, crystals were soaked overnight with two fragment libraries; the Diamond- SGC Poised Library set (Cox et al., 2016) and the &lt;a href="https://xchem.github.io/oxxchem/"&gt;OxXChem&lt;/a&gt; set with nominal fragment concentrations of 100 mM, with DMSO at 30% v/v. Additionally, a series of follow-up compounds based on an initial fragment hit was synthesized and soaked overnight with nominal compound concentrations of 30 mM, with DMSO at 30% v/v. All datasets were collected at &lt;a href="http://www.diamond.ac.uk/Beamlines/Mx.html"&gt;MX beamlines at DLS&lt;/a&gt;. Autoprocessed datasets were analysed by Pan-Dataset Density Analysis (PanDDA) (Pearce et al., 2017). All ligands that were clearly identifiable in PanDDA event maps were modelled, refined and deposited into the PDB.&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&lt;strong&gt;Content&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;This repository contains:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;all results from the PanDDA analysis, including ground-state-mean maps and PanDDA event &amp;amp; Z-maps for all ligand bound structures&lt;/li&gt;
	&lt;li&gt;MTZ and AIMLESS logfiles from auto-processing&lt;/li&gt;
	&lt;li&gt;PDB, CIF &amp;amp; PNG files of all the soaked compounds&lt;/li&gt;
	&lt;li&gt;final refine.pdb and refine.mtz filess of all ligand bound structures&lt;/li&gt;
	&lt;li&gt;all data belonging to an individual crystal can be found in &lt;em&gt;processed_datasets/&amp;lt;crystal_ID&amp;gt;&lt;/em&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;Cox, O. B. et al. A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem. Sci. 7, 2322&amp;ndash;2330 (2016).&lt;/p&gt;

&lt;p&gt;Pearce, N. M. et al. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 8, (2017).&lt;/p&gt;</description>
  </descriptions>
</resource>