A procedure for ab initio phasing of one-wavelength anomalous scattering data from proteins – combining direct methods with the solvent flattening technique

1997 ◽  
Vol 212 (2) ◽  
Author(s):  
X. F. Zheng ◽  
Y. X. Gu ◽  
C. D. Zheng ◽  
Y. D. Mo ◽  
H. F. Fan ◽  
...  
Keyword(s):  
Ab Initio ◽  
Diffraction Data ◽  
Direct Method ◽  
Direct Methods ◽  
Special Care ◽  
Scattering Data ◽  
Anomalous Scattering ◽  
Phase Ambiguity ◽  
Moderate Size ◽  
Subsequent Phase

AbstractBoth direct methods and the solvent flattening technique have been proved capable of breaking the phase ambiguity intrinsic in one-wavelength anomalous scattering (OAS) data. However, in theory, while direct methods are better in deriving starting phases from OAS data, the solvent flattening technique is more powerful in the subsequent phase refinement. A procedure is described in this paper which combines direct methods with the solvent flattening technique for phasing of OAS data. The procedure has been tested with the known protein RNase Sa. This protein is of moderate size, and the diffraction data were collected routinely without taking special care for the recording of Friedels. The test proved that the combination of the direct method and the solvent flattening leads to a much better result than that from either method alone.

Combining direct methods with isomorphous replacement or anomalous scattering data. VIII. Phasing experimental SIR data with the replacing atoms in a centrosymmetric arrangement

1999 ◽  
Vol 55 (4) ◽  
pp. 846-848 ◽  
Author(s):  
Yu-Dong Liu ◽  
Yuan-Xin Gu ◽  
Chao-De Zheng ◽  
Q. Hao ◽  
Hai-Fu Fan
Keyword(s):  
Cluster Analysis ◽  
Phase Difference ◽  
Direct Method ◽  
Direct Methods ◽  
Scattering Data ◽  
Anomalous Scattering ◽  
Phase Ambiguity ◽  
Native Protein ◽  
Figures Of Merit ◽  
Isomorphous Replacement

A multisolution direct method has been proposed to resolve the phase ambiguity intrinsic in single isomorphous replacement data of proteins with the replacing atoms in a centrosymmetric arrangement. The phase ambiguity of each reflection is in fact a `sign ambiguity' of the phase difference between the phase of the native protein and that of the replacing atoms, i.e. ± |Δφ| = φ − φ′. The P + probability formula can be used to derive the signs. The multisolution phasing procedure is initiated using random starting values of P +. A cluster analysis is used instead of figures of merit to find the correct solution. The direct-method phases can be further improved by density-modification techniques. The method was tested with the experimental SIR data at 2 Å resolution from a known protein aPP; satisfactory results were obtained.

A case study on the treatment of protein SIRAS data

2014 ◽  
Vol 70 (10) ◽  
pp. 2686-2691 ◽  
Author(s):  
Deqiang Yao ◽  
Tao Zhang ◽  
Yao He ◽  
Pu Han ◽  
Maia Cherney ◽  
...  
Keyword(s):  
Direct Method ◽  
Direct Methods ◽  
Phase Model ◽  
Protein Crystal ◽  
Scattering Data ◽  
Anomalous Scattering ◽  
Data Set ◽  
Model Extension ◽  
Sad Phasing

A case study has been made on the treatment of the SIRAS (single isomorphous replacement with anomalous scattering) data of the originally unknown protein LegC3N. An alternative treatment has been proposed which led to improved results in this particular test case. The treatment involves iterative direct-method SAD (single-wavelength anomalous diffraction) phasing and direct-method-aided model completion, both of which are implanted in theIPCAS(Iterative Protein Crystal-structure Automatic Solution) pipeline. Apart from the experimental data, a simulated SIRAS data set for LegC3N with the derivative data truncated to 5.0 Å resolution has also been tested. SAD phasing and phase/model extension inPHENIXwithout direct methods failed to solve the structure using these simulated SIRAS data. However, the procedure proposed here involving direct methods in both SAD phasing and phase/model extension led to a nearly complete structure model. This shows the potential ability of treating SIRAS data with a derivative diffracting to lower resolution.

Direct-method phasing of anomalous diffraction from proteins

2002 ◽  
Vol 217 (12) ◽  
Author(s):  
Y. X. Gu ◽  
F. Jiang ◽  
B. D. Sha ◽  
H. F. Fan
Keyword(s):  
Protein Structure ◽  
Probability Distribution ◽  
Direct Method ◽  
Direct Methods ◽  
Phase Ambiguity ◽  
Anomalous Diffraction ◽  
Additional Information ◽  
Mad Phasing ◽  
Three Phase ◽  
Multi Wavelength

AbstractIn dealing with anomalous diffraction data from proteins, the probability distribution of three-phase structure invariants provides additional information, which can be used to resolve the phase ambiguity intrinsic in single-wavelength anomalous diffraction (SAD) enabling solution of the protein structure. Based on this, direct methods have also been used in phasing multi-wavelength anomalous diffraction (MAD) data leading to better result than that from the conventional MAD phasing.

Ab initio structure determination of monoclinic 2,2-dihydroxymethylbutanoic acid from synchrotron radiation powder diffraction data: combined use of direct methods and the Monte Carlo method

2001 ◽  
Vol 57 (2) ◽  
pp. 184-189 ◽  
Author(s):  
Yusaku Tanahashi ◽  
Hisayoshi Nakamura ◽  
Satoru Yamazaki ◽  
Yuko Kojima ◽  
Hideshi Saito ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Method ◽  
Synchrotron Radiation ◽  
Ab Initio ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Rietveld Method ◽  
Direct Methods ◽  
Powder Diffraction Data ◽  
The Monte Carlo Method

The crystal structure of 2,2-dihydroxymethylbutanoic acid (C6H12O4) in monoclinic form has been determined ab initio from synchrotron radiation powder diffraction data. Two O and five C atoms were first derived by direct methods. Two missing O atoms and one C atom were found by the Monte Carlo method without applying constraint to their relative positions. Positional and isotropic displacement parameters of these non-H atoms were refined by the Rietveld method. Molecules are linked by hydrogen bonds and they make sheet-like networks running parallel to the (010) plane. The Monte Carlo method is demonstrated to be a powerful tool for finding missing atoms in partially solved structure.

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