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000009741 0247_ $$2DOI$$a10.1038/nature08892
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000009741 084__ $$2WoS$$aMultidisciplinary Sciences
000009741 1001_ $$0P:(DE-Juel1)132018$$aSchröder, G.F.$$b0$$uFZJ
000009741 245__ $$aSuper-resolution biomolecular crystallography with low-resolution data
000009741 260__ $$aLondon [u.a.]$$bNature Publising Group$$c2010
000009741 300__ $$a1218 - 1222
000009741 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article
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000009741 3367_ $$2BibTeX$$aARTICLE
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000009741 440_0 $$04484$$aNature$$v464$$x0028-0836
000009741 500__ $$aWe thank P. D. Adams, S. C. Harrison and T. D. Fenn for discussions. We also thank the National Science Foundation for computing resources (CNS-0619926), the National Institutes of Health for both Roadmap Grant PN2 (EY016525) and grant GM63718 to M. L., and the Deutsche Forschungsgemeinschaft (DFG) for support for G. F. S.
000009741 520__ $$aX-ray diffraction plays a pivotal role in the understanding of biological systems by revealing atomic structures of proteins, nucleic acids and their complexes, with much recent interest in very large assemblies like the ribosome. As crystals of such large assemblies often diffract weakly (resolution worse than 4 A), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, whereas others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining the structure of such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution better than 5 A generally exceeds the number of degrees of freedom. Here we introduce a method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with R(free) (the free R-factor) determines the optimum deformation and influence of the homology model. For test cases at 3.5-5 A resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model as monitored by coordinate accuracy, the definition of secondary structure and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the Protein Data Bank, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to the study of weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X-ray crystallography and cryo-electron microscopy: as optical imaging advances to subnanometre resolution, it can use similar tools.
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000009741 536__ $$0G:(DE-Juel1)FUEK505$$2G:(DE-HGF)$$aBioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung$$cP45$$x1
000009741 588__ $$aDataset connected to Web of Science, Pubmed
000009741 650_2 $$2MeSH$$aCrystallization
000009741 650_2 $$2MeSH$$aCrystallography, X-Ray: methods
000009741 650_2 $$2MeSH$$aDatabases, Protein
000009741 650_2 $$2MeSH$$aElectrons
000009741 650_2 $$2MeSH$$aLikelihood Functions
000009741 650_2 $$2MeSH$$aModels, Molecular
000009741 650_2 $$2MeSH$$aOligopeptides: chemistry
000009741 650_2 $$2MeSH$$aProtein Conformation
000009741 650_2 $$2MeSH$$aSoftware
000009741 650_2 $$2MeSH$$aStatic Electricity
000009741 650_7 $$00$$2NLM Chemicals$$aOligopeptides
000009741 650_7 $$2WoSType$$aJ
000009741 7001_ $$0P:(DE-HGF)0$$aLevitt, M.$$b1
000009741 7001_ $$0P:(DE-HGF)0$$aBrunger, A.T.$$b2
000009741 773__ $$0PERI:(DE-600)1413423-8$$a10.1038/nature08892$$gVol. 464, p. 1218 - 1222$$p1218 - 1222$$q464<1218 - 1222$$tNature <London>$$v464$$x0028-0836$$y2010
000009741 8567_ $$2Pubmed Central$$uhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859093
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000009741 9131_ $$0G:(DE-Juel1)FUEK505$$aDE-HGF$$bSchlüsseltechnologien$$kP45$$lBiologische Informationsverarbeitung$$vBioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung$$x1
000009741 9132_ $$0G:(DE-HGF)POF3-551$$1G:(DE-HGF)POF3-550$$2G:(DE-HGF)POF3-500$$aDE-HGF$$bKey Technologies$$lBioSoft  Fundamentals for future Technologies in the fields of Soft Matter and Life Sciences$$vFunctional Macromolecules and Complexes$$x0
000009741 9201_ $$0I:(DE-Juel1)VDB942$$d31.12.2010$$gISB$$kISB-3$$lStrukturbiochemie$$x0
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