Density modification for macromolecular phase improvement - PubMed (original) (raw)
Density modification for macromolecular phase improvement
K D Cowtan et al. Prog Biophys Mol Biol. 1999.
Free article
Abstract
Density modification provides a simple and largely automatic tool for improving phase estimates for observed structure factors. The phase information arises from a combination of the known structure factor magnitudes, the current phase estimates, and stereochemical information. The magnitudes, the current phase estimates, and stereochemical information. The addition of these phase information derived from theoretical sources renders new structures amenable to solution, and reduces the effort required to solve other structures. A diverse array of techniques which have been applied to the phase improvement problem are reviewed.
Similar articles
- Phasing methods for protein crystallography.
Hauptman H. Hauptman H. Curr Opin Struct Biol. 1997 Oct;7(5):672-80. doi: 10.1016/s0959-440x(97)80077-2. Curr Opin Struct Biol. 1997. PMID: 9345626 Review. - CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography.
Thireou T, Atlamazoglou V, Levakis M, Eliopoulos E, Hountas A, Tsoucaris G, Bethanis K. Thireou T, et al. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W718-22. doi: 10.1093/nar/gkm225. Epub 2007 May 8. Nucleic Acids Res. 2007. PMID: 17488848 Free PMC article. - Synergy among phase-refinement techniques in macromolecular crystallography.
Burla MC, Cascarano GL, Giacovazzo C, Polidori G. Burla MC, et al. Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):877-888. doi: 10.1107/S2059798317014590. Epub 2017 Oct 19. Acta Crystallogr D Struct Biol. 2017. PMID: 29095160 - CAB: a cyclic automatic model-building procedure.
Burla MC, Carrozzini B, Cascarano GL, Polidori G, Giacovazzo C. Burla MC, et al. Acta Crystallogr D Struct Biol. 2018 Nov 1;74(Pt 11):1096-1104. doi: 10.1107/S2059798318013438. Epub 2018 Oct 29. Acta Crystallogr D Struct Biol. 2018. PMID: 30387768 - Structure Refinement at Atomic Resolution.
Jaskolski M. Jaskolski M. Methods Mol Biol. 2017;1607:549-563. doi: 10.1007/978-1-4939-7000-1_22. Methods Mol Biol. 2017. PMID: 28573588 Review.
Cited by
- Structure of human cytomegalovirus UL141 binding to TRAIL-R2 reveals novel, non-canonical death receptor interactions.
Nemčovičová I, Benedict CA, Zajonc DM. Nemčovičová I, et al. PLoS Pathog. 2013 Mar;9(3):e1003224. doi: 10.1371/journal.ppat.1003224. Epub 2013 Mar 21. PLoS Pathog. 2013. PMID: 23555243 Free PMC article. - A multi-faceted analysis of RutD reveals a novel family of α/β hydrolases.
Knapik AA, Petkowski JJ, Otwinowski Z, Cymborowski MT, Cooper DR, Majorek KA, Chruszcz M, Krajewska WM, Minor W. Knapik AA, et al. Proteins. 2012 Oct;80(10):2359-68. doi: 10.1002/prot.24122. Epub 2012 Jun 30. Proteins. 2012. PMID: 22641504 Free PMC article. - The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation.
Mueller-Dieckmann C, Kernstock S, Lisurek M, von Kries JP, Haag F, Weiss MS, Koch-Nolte F. Mueller-Dieckmann C, et al. Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15026-31. doi: 10.1073/pnas.0606762103. Epub 2006 Oct 2. Proc Natl Acad Sci U S A. 2006. PMID: 17015823 Free PMC article. - X-ray structure of Paramecium bursaria Chlorella virus arginine decarboxylase: insight into the structural basis for substrate specificity.
Shah R, Akella R, Goldsmith EJ, Phillips MA. Shah R, et al. Biochemistry. 2007 Mar 13;46(10):2831-41. doi: 10.1021/bi6023447. Epub 2007 Feb 17. Biochemistry. 2007. PMID: 17305368 Free PMC article. - Crystal structure of the middle and C-terminal domains of the flagellar rotor protein FliG.
Brown PN, Hill CP, Blair DF. Brown PN, et al. EMBO J. 2002 Jul 1;21(13):3225-34. doi: 10.1093/emboj/cdf332. EMBO J. 2002. PMID: 12093724 Free PMC article.