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dc.contributor.authorHatti, Kaushiken
dc.contributor.authorMcCoy, Airlieen
dc.contributor.authorOeffner, Roberten
dc.contributor.authorSammito, Massimoen
dc.contributor.authorRead, Randyen
dc.date.accessioned2019-11-23T00:31:39Z
dc.date.available2019-11-23T00:31:39Z
dc.date.issued2020-01en
dc.identifier.issn2059-7983
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/299196
dc.description.abstractGood prior estimates of the effective root-mean-square deviation (RMSD) between atomic coordinates of the model and the target optimise the signal in molecular replacement, thereby increasing the success rate in difficult cases. Previous studies using protein structures solved by X-ray crystallography as models showed that optimal error estimates (refined after structure solution) were correlated with sequence identity between the model and target, and with the number of residues in the model. Here we have extended this work to find additional correlations between parameters of the model and target and hence improved prior estimates of the coordinate error. Using a graph database, a curated set of 6,030 molecular replacement calculations using models that had been solved by X-ray crystallography was analysed to consider about 120 model and target parameters. Improved estimates were achieved by replacing the sequence identity with the Gonnet score for sequence similarity, as well as by considering the resolution of the target structure and the MolProbity score of the model. This approach was extended by analysing 12,610 additional molecular replacement calculations where the model was determined by NMR. The median RMSD between pairs of models in an ensemble was found to be correlated with the estimated RMSD to the target. For models solved by NMR, the overall coordinate error estimates were larger than for structures determined by X-ray crystallography, and were more highly correlated with the number of residues.
dc.format.mediumPrint-Electronicen
dc.languageengen
dc.publisherBlackwell Publishing Inc.
dc.rightsAll rights reserved
dc.subjectProteinsen
dc.subjectCrystallography, X-Rayen
dc.subjectMagnetic Resonance Spectroscopyen
dc.subjectProtein Conformationen
dc.subjectModels, Molecularen
dc.titleFactors influencing estimates of coordinate error for molecular replacement.en
dc.typeArticle
prism.endingPage27
prism.issueIdentifierPt 1en
prism.publicationDate2020en
prism.publicationNameActa crystallographica. Section D, Structural biologyen
prism.startingPage19
prism.volume76en
dc.identifier.doi10.17863/CAM.46261
dcterms.dateAccepted2019-11-21en
rioxxterms.versionofrecord10.1107/s2059798319015730en
rioxxterms.versionAM
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2020-01en
dc.contributor.orcidHatti, Kaushik [0000-0002-6779-7283]
dc.contributor.orcidOeffner, Robert [0000-0003-3107-2202]
dc.contributor.orcidSammito, Massimo [0000-0002-8346-9247]
dc.contributor.orcidRead, Randy [0000-0001-8273-0047]
dc.identifier.eissn2059-7983
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idNational Institutes of Health (NIH) (via University of California) (6801943)
pubs.funder-project-idSTFC (unknown)
pubs.funder-project-idEuropean Commission Horizon 2020 (H2020) Marie Sklodowska-Curie actions (790122)
pubs.funder-project-idWellcome Trust (209407/Z/17/Z)
pubs.funder-project-idWellcome Trust (082961/Z/07/A)
pubs.funder-project-idBBSRC (BB/L006014/1)
pubs.funder-project-idNational Institute of General Medical Sciences (P01GM063210)
cam.orpheus.successTue Sep 01 14:03:25 BST 2020 - Embargo updated*
rioxxterms.freetoread.startdate2020-01-31


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