SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS
He Yao(何尧)a), Gu Yuan-Xin(古元新)a)† , Lin Zheng-Jiong(林政炯)a)b), Zheng Chao-De(郑朝德)a), and Fan Hai-Fu(范海福)a)
a Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China; b Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
Abstract 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.
Received: 16 July 2007
Revised: 17 July 2007
Accepted manuscript online:
(Folding: thermodynamics, statistical mechanics, models, and pathways)
Fund: Project
supported by the Innovation Project of the Chinese Academy
of Sciences and the 973 Project(Grant No~2002CB713801)
of the Ministry of Science and Technology of China.
Cite this article:
He Yao(何尧), Gu Yuan-Xin(古元新), Lin Zheng-Jiong(林政炯), Zheng Chao-De(郑朝德), and Fan Hai-Fu(范海福) SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS 2007 Chinese Physics 16 3022
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