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 lo...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-Kα 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-Kα sulfur-SAD data have an expected Bijvoet ratio 〈 ｜△F｜ 〉 / 〈 F 〉 ～ 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.展开更多
The program OASIS4.0 has been released. Apart from the improved single-wavelength anomalous diffraction （SAD） phasing algorithm described in a separate paper, an important new feature in this version is the automati...The program OASIS4.0 has been released. Apart from the improved single-wavelength anomalous diffraction （SAD） phasing algorithm described in a separate paper, an important new feature in this version is the automation of the iterative phasing and model-building process in solving protein structures. A new graphical user＇s interface （GUI） is provided for controlling and real-time monitoring the dual-space iterative process. The GUI is discussed in detail in the present paper.展开更多
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. Tw...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.展开更多
基金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
文摘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-Kα 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-Kα sulfur-SAD data have an expected Bijvoet ratio 〈 ｜△F｜ 〉 / 〈 F 〉 ～ 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.
基金Project supported by the Innovation Foundation of the Chinese Academy of Sciences,and the National Basic Research Program of China(Grant No.2002CB713801)
文摘The program OASIS4.0 has been released. Apart from the improved single-wavelength anomalous diffraction （SAD） phasing algorithm described in a separate paper, an important new feature in this version is the automation of the iterative phasing and model-building process in solving protein structures. A new graphical user＇s interface （GUI） is provided for controlling and real-time monitoring the dual-space iterative process. The GUI is discussed in detail in the present paper.
文摘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.
