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000133925 1001_ $$0P:(DE-HGF)0$$aDas, Debanu$$b0
000133925 245__ $$aApplication 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
000133925 260__ $$aCopenhagen$$bMunksgaard$$c2012
000133925 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article$$bjournal$$mjournal$$s1374675965_27989
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000133925 520__ $$aPhasing 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 Ang 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.
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000133925 7001_ $$0P:(DE-HGF)0$$aDeacon, Ashley M.$$b1
000133925 7001_ $$0P:(DE-HGF)0$$aGrant, Joanna$$b2
000133925 7001_ $$0P:(DE-HGF)0$$aTerwilliger, Thomas C.$$b3
000133925 7001_ $$0P:(DE-HGF)0$$aRead, Randy J.$$b4
000133925 7001_ $$0P:(DE-HGF)0$$aAdams, Paul D.$$b5
000133925 7001_ $$0P:(DE-HGF)0$$aLevitt, Michael$$b6
000133925 7001_ $$0P:(DE-Juel1)132018$$aSchröder, Gunnar$$b7$$ufzj
000133925 7001_ $$0P:(DE-HGF)0$$aBrunger, Axel T.$$b8$$eCorresponding author
000133925 773__ $$0PERI:(DE-600)2020492-9$$a10.1107/S090744491104978X$$n4$$p391 - 403$$tActa crystallographica / D$$v68
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000133925 9132_ $$0G:(DE-HGF)POF3-559H$$1G:(DE-HGF)POF3-550$$2G:(DE-HGF)POF3-500$$aDE-HGF$$bKey Technologies$$lBioSoft – Fundamentals for future Technologies in the fields of Soft Matter and Life Sciences$$vAddenda$$x0
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