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	SAD phasing by OASIS at different resolutions down to 0.30 nm and below
	Yao DeQiang; Li He; Chen Qiang; Gu YuanXin; Zheng ChaoDe; Lin ZhengJiong; Fan HaiFu; Nobuhisa Watanabe; Sha BingDong
来源期刊	Chinese Physics. B
ISSN	1674-1056
出版年	2008
卷号	17 期号:1 页码:1-9
英文摘要	Single-wavelength anomalous diffraction (SAD) phasing is increasingly important in solving de novo protein structures. Direct methods have been proved very efficient in SAD phasing. This paper aims at probing the low-resolution limit of direct-method SAD phasing. Two known proteins TT0570 and Tom70p were used as test samples. Sulfur-SAD data of the protein TT0570 were collected with conventional Cu-Kalpha source at 0.18 nm resolution. Its truncated subsets respectively at 0.21, 0.30, 0.35 and 0.40 nm resolutions were used in the test. TT0570 Cu-Kalpha sulfur-SAD data have an expected Bijvoet ratio <\|DeltaF\|> / ~ 0.55%. In the 0.21 nm case, a single run of OASIS-DM-ARP/wARP led automatically to a model containing 1178 of the total 1206 residues all docked into the sequence. In 0.30 and 0.35 nm cases, SAD phasing by OASIS-DM led to traceable electron density maps. In the 0.40 nm case, SAD phasing by OASIS-DM resulted in a degraded electron density map, which may be difficult to trace but still contains useful secondary-structure information. Test on real 0.33 nm selenium-SAD data of the protein Tom70p showed that even automatic model building was not successful, the combination of manual tracing and direct-method fragment extension was capable of significantly improving the electron-density map. This provides the possibility of effectively improving the manually built model before structure refinement is performed.
英文关键词	OASIS SAD phasing dual-space fragment extension proteins
类型	Article
语种	英语
收录类别	CSCD
WOS研究方向	Physics
CSCD记录号	CSCD:3251033
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/334967
作者单位	Yao DeQiang, 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.; Zheng ChaoDe, 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.; Fan HaiFu, Institute of Physics, Chinese Academy of Sciences, Beijing National Laboratory for Condensed Matter Physics, Beijing 100080, China.; Li He, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.; Chen Qiang, Peking University, National Laboratory of Protein Engineering and Plant Genetic Engineering, Beijing 100871, China.; Nobuhisa Watanabe, Department of Biotechnology and Biomaterial Chemistry, N...
推荐引用方式 GB/T 7714	Yao DeQiang,Li He,Chen Qiang,et al. SAD phasing by OASIS at different resolutions down to 0.30 nm and below[J],2008,17(1):1-9.
APA	Yao DeQiang.,Li He.,Chen Qiang.,Gu YuanXin.,Zheng ChaoDe.,...&Sha BingDong.(2008).SAD phasing by OASIS at different resolutions down to 0.30 nm and below.Chinese Physics. B,17(1),1-9.
MLA	Yao DeQiang,et al."SAD phasing by OASIS at different resolutions down to 0.30 nm and below".Chinese Physics. B 17.1(2008):1-9.