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SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS

Yao He,Yuanxin Gu,ZhengJiong Lin,ChaoDe Zheng,HaiFu Fan,何 尧, 古元新, 林政炯, 郑朝德, 范海福

CHINESE PHYSICS(2007)

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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: ILIA) 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.
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关键词
sIR phasing,SOLVE/RESOLVE,OASIS,dual-space fragment extension for proteins
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