Improving experimental phases for strong reflections prior to density modification

doi:10.1107/S0907444913018167

	Improving experimental phases for strong reflections prior to density modification
	Uervirojnangkoorn, Monarin 2,3; Hilgenfeld, Rolf 2,4; Terwilliger, Thomas C.1,5; Read, Randy J.6
刊名	ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
	2013-10
卷号	69 页码:2039-2049
ISSN号	0907-4449
DOI	10.1107/S0907444913018167
文献子类	Article
英文摘要	Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [ Vekhter (2005), Acta Cryst. D61, 899-902], the impact of identifying optimized phases for a small number of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. A computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.
资助项目	Graduate School for Computing in Medicine and Life Sciences[DFG GSC 235/1] ; Cluster of Excellence 'Inflammation at Interfaces'[DFG EXC 306/2] ; NIH[P01GM063210] ; Wellcome Trust[082961] ; Chinese Academy of Sciences through a Visiting Professorship for Senior International Scientists[2010T1S6]
WOS关键词	POWDER DIFFRACTION DATA ; GENETIC ALGORITHM ; CRYSTAL-STRUCTURE ; CRYSTALLOGRAPHY ; RESOLUTION ; ERRORS ; PHENIX ; RNA
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics ; Crystallography
语种	英语
出版者	WILEY-BLACKWELL
WOS记录号	WOS:000325403900017
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/277439]
专题	中国科学院上海药物研究所
通讯作者	Hilgenfeld, Rolf
作者单位	1.Los Alamos Natl Lab, Los Alamos Inst, Los Alamos, NM 87545 USA; 2.Med Univ Lubeck, Ctr Struct & Cell Biol Med, Inst Biochem, D-23538 Lubeck, Germany; 3.Med Univ Lubeck, Grad Sch Comp Med & Life Sci, D-23538 Lubeck, Germany; 4.Chinese Acad Sci, Shanghai Inst Mat Med, Shanghai 201203, Peoples R China; 5.Los Alamos Natl Lab, Biosci Div, Los Alamos, NM 87545 USA; 6.Univ Cambridge, Cambridge Inst Med Res, Dept Haematol, Cambridge CB2 0XY, England
推荐引用方式 GB/T 7714	Uervirojnangkoorn, Monarin,Hilgenfeld, Rolf,Terwilliger, Thomas C.,et al. Improving experimental phases for strong reflections prior to density modification[J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY,2013,69:2039-2049.
APA	Uervirojnangkoorn, Monarin,Hilgenfeld, Rolf,Terwilliger, Thomas C.,&Read, Randy J..(2013).Improving experimental phases for strong reflections prior to density modification.ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY,69,2039-2049.
MLA	Uervirojnangkoorn, Monarin,et al."Improving experimental phases for strong reflections prior to density modification".ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 69(2013):2039-2049.