干旱区生态环境知识资源中心(Arid): SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS

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	SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS
	He Yao; Gu YuanXin; Lin ZhengJiong; Zheng ChaoDe; Fan HaiFu
来源期刊	Chinese Physics
ISSN	1009-1963
出版年	2007
卷号	16 期号:10 页码:3022-3028
英文摘要	A new phasing procedure has been proposed for dealing with single isomorphous replacement (SIR) x-ray diffraction data. The procedure combines SOLVE/RESOLVE with the dual-space fragment extension involving OASIS. Two sets of SIR data at 0.28 nm resolution taken from the protein (R)-phycoerythrin (PDB code: 1LIA) were used in the test. For one of the two SIR data sets, a default run of SOLVE/RESOLVE based on the heavy-atom substructure found by SHLEXD led automatically to an interpretable electron density map. OASIS could not effectively improve the result. For the other set of SIR data, SOLVE/RESOLVE resulted in a fragmented model consisting of 454 of the total 668 residues, in which only 29 residues were docked into the sequence. Based on this model, 7 iteration cycles of OASIS-DM-RESOLVE (build only) yielded automatically a model of 547 residues with 133 residues docked into the sequence. The overall-averaged phase error decreased considerably and the quality of electron density map was improved significantly. Two more cycles of iterative OASIS-DM-RESOLVE were carried out, in which the output phases and figures of merit from DM were merged with that from the original run of SOLVE/RESOLVE before they were passed onto RESOLVE (build only). This led automatically to a model containing 452 residues with 173 docked into the sequence. The resultant electron density map is manually traceable. It is concluded that when results of SOLVE/RESOLVE are not sufficiently satisfactory, the combination of SOLVE/RESOLVE and OASIS-DM-RESOLVE (build only) may significantly improve them.
英文关键词	SIR phasing SOLVE/RESOLVE OASIS dual-space fragment extension for proteins
类型	Article
语种	英语
收录类别	CSCD
WOS研究方向	Physics
CSCD记录号	CSCD:3131669
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/334954
作者单位	He Yao, Institute of Physics, Chinese Academy of Sciences, Beijing National Laboratory for Condensed Matter Physics, Beijing 100080, China.; Gu YuanXin, Institute of Physics, Chinese Academy of Sciences, Beijing National Laboratory for Condensed Matter Physics, Beijing 100080, China.; Lin ZhengJiong, Institute of Physics, Chinese Academy of Sciences, Beijing National Laboratory for Condensed Matter Physics, Beijing 100080, China.; Zheng ChaoDe, Institute of Physics, Chinese Academy of Sciences, Beijing National Laboratory for Condensed Matter Physics, Beijing 100080, China.; Fan HaiFu, Institute of Physics, Chinese Academy of Sciences, Beijing National Laboratory for Condensed Matter Physics, Beijing 100080, China.
推荐引用方式 GB/T 7714	He Yao,Gu YuanXin,Lin ZhengJiong,et al. SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS[J],2007,16(10):3022-3028.
APA	He Yao,Gu YuanXin,Lin ZhengJiong,Zheng ChaoDe,&Fan HaiFu.(2007).SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS.Chinese Physics,16(10),3022-3028.
MLA	He Yao,et al."SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS".Chinese Physics 16.10(2007):3022-3028.