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Phasing of lysozyme using one-wavelength anomalous scattering of sulphur atoms through the combination of direct methods and density modification 下载免费PDF全文
A new method of combining one-wavelength anomalous scattering (OAS) phasing and density modification has been described, in which the improved phases from density modification axe re-introduced into OAS phasing. In this way, the phases could be improved iteratively until convergence. The OAS phasing method is based on the previously established sign-probability formula, which breaks the phase ambiguity in the OAS phasing. The implementation of this method has been available in CCP4 as OASIS. This method, although based on direct-methods, could also incorporate known phases and figures of merit into its sign-probability formula. In the implementation of OASIS, the known phases axe from the positions of the anomalous scatters. In the current method, the known phases are from the density modification. The current method was tested on phasing a lysozyme crystal using anomalous scattering of sulphur atoms with diffraction data collected on an in-house x-ray source. The resulting map was well connected for the backbone atoms and clearly traceable, with an average map correlation coefficient of 0.6622 for the backbone atoms. 相似文献
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SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS 下载免费PDF全文
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. 相似文献
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There are two kinds of dual-space partial-model extensions which involve the direct-method program OASIS. The first kind, named SAD/SIR iteration, uses SAD/SIR information, while the second kind, named molecular replacement (MR) iteration, does not use that information. In general, the SAD/SIR iteration is more powerful since more experimental information is used. However, in most cases when protein structures are solved with the molecular replacement method, SAD/SIR information is not available. Thus the MR iteration is particularly useful for the completion of models from molecular replacement. The SAD/SIR iteration will be automatically used in OASIS for data sets containing SAD/SIR signals, while the MR iteration will be dedicated to data sets without SAD/SIR signals. The present paper shows that for data containing SAD/SIR signals, a combination of SAD/SIR iteration and MR iteration could lead to significantly better results than that obtained from the SAD/SIR iteration alone. 相似文献
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<正>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. 相似文献
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Ab-initio determination of the incommensurate modulated structure of Bi-2212 from x-ray powder diffraction data -a simulation 下载免费PDF全文
A set of x-ray powder diffraction data of the high-T_c superconductor Bi_2Sr_2Ca_1Cu_2O_y (Bi-2212) was simulated based on the experimental single-crystal diffraction data by merging together reflections with diffraction angles (2θ) closer to each other than 0.04 degrees. There are three types of overlapping in the powder diffraction data, i.e. (i) overlapping of main reflections; (ii) overlapping of satellite reflections and (iii) overlapping of main and satellite reflections. The third type of overlapping was first separated into main and satellite components according to the ratio between the average intensity of that of types (i) and (ii). Then the overlapped reflections of main reflections and those of the satellites were uniformly partitioned. Heavy-atom sites in the basic/average structure were found using the uniformly decomposed main reflections by the conventional direct method. Phases of the satellites were derived by the multidimensional direct method. The resultant four-dimensional Fourier maps revealed correctly the essential feature of the modulation. No assumption on either the basic structure or the modulation is needed. 相似文献