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SAD phasing by OASIS at different resolutions down to 0.30nm and below
姚德强, 李鹤, 陈强, 古元新, 郑朝德, 林政炯, 范海福, 渡邉信久, 沙炳东
2008 (1):
1-9.
doi: 10.1088/1674-1056/17/1/001
摘要
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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-K\alpha source at 0.18nm resolution. Its
truncated subsets respectively at 0.21, 0.30, 0.35 and 0.40nm
resolutions were used in the test. TT0570 Cu-K$\alpha$ sulfur-SAD
data have an expected Bijvoet ratio <\vert\Delta F\vert>/\ \sim
0.55%. In the 0.21nm 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 0.35nm cases,
SAD phasing by OASIS-DM led to traceable electron density maps. In
the 0.40nm 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
0.33nm 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.
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