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dc.contributor.authorBrunger, Axel T
dc.contributor.authorDas, Debanu
dc.contributor.authorDeacon, Ashley M
dc.contributor.authorGrant, Joanna
dc.contributor.authorTerwilliger, Thomas C
dc.contributor.authorRead, Randy
dc.contributor.authorAdams, Paul D
dc.contributor.authorLevitt, Michael
dc.contributor.authorSchröder, Gunnar F
dc.date.accessioned2020-05-11T23:31:09Z
dc.date.available2020-05-11T23:31:09Z
dc.date.issued2012-04
dc.identifier.issn0907-4449
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/305232
dc.description.abstractPhasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.
dc.format.mediumPrint-Electronic
dc.languageeng
dc.publisherInternational Union of Crystallography (IUCr)
dc.rightsAll rights reserved
dc.subjectCorynebacterium glutamicum
dc.subjectAmidohydrolases
dc.subjectCrystallography, X-Ray
dc.subjectSequence Alignment
dc.subjectAmino Acid Sequence
dc.subjectStructural Homology, Protein
dc.subjectModels, Molecular
dc.subjectSoftware
dc.subjectMolecular Sequence Data
dc.subjectAutomation, Laboratory
dc.titleApplication of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.
dc.typeArticle
prism.endingPage403
prism.issueIdentifierPt 4
prism.publicationDate2012
prism.publicationNameActa Crystallogr D Biol Crystallogr
prism.startingPage391
prism.volume68
dc.identifier.doi10.17863/CAM.52319
dcterms.dateAccepted2011-11-21
rioxxterms.versionofrecord10.1107/S090744491104978X
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.licenseref.startdate2012-04
dc.contributor.orcidRead, Randy [0000-0001-8273-0047]
dc.identifier.eissn1399-0047
rioxxterms.typeJournal Article/Review
pubs.funder-project-idWellcome Trust (082961/Z/07/Z)
pubs.funder-project-idNational Institute of General Medical Sciences (P01GM063210)
cam.issuedOnline2012-03-16


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