One-wavelength Anomalous Scattering Research Articles

Phasing of lysozyme using one-wavelength anomalous scattering of sulphur atoms through the combination of direct methods and density modification

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 are 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 are 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.

Phasing of lysozyme using one-wavelength anomalous scattering of sulphur atoms through the combination of direct methods and density modification

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 are 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 are 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.

Direct-method-aided phasing of MAD data

The direct methods of breaking the phase ambiguity intrinsic in one-wavelength anomalous scattering (OAS) data and MAD phasing are powerful methods in their own rights. In a different context, in addition to their success in phasing OAS data, direct methods can also be useful in the treatment of MAD data. The idea has been tested with the MAD data at 2.5 A resolution from the protein human adenosine kinase [Mathews et al. (1998), Biochemistry, 37, 15607--15620]. The results showed that the incorporation of direct methods in MAD phasing led to a significant improvement of phases over those obtained from the conventional MAD phasing method alone, as indicated by improved map correlation coefficients (with the existing model), reduced phase errors by 4.5 degrees and improved map connectivity.

The method of joint probability distribution functions applied to the one-wavelength anomalous-scattering (OAS) case.

The method of the joint probability distribution function is applied to the case in which the positions of the anomalous scatterers are fully or partially known. The mathematical technique is able to handle errors both in the model structure of the located anomalous scatterers and in measurements. A criterion for ranking the more accurate phase estimates is given.

OASIS: a computer program for breaking phase ambiguity in one-wavelength anomalous scattering or single isomorphous substitution (replacement) data

The phase problem is reduced to a sign problem once the anomalous-scatterer or the replacing-heavy-atom sites are located.OASISadopts theCCP4 format [Collaborative Computational Project, Number 4 (1994).Acta Cryst.D50, 760–763]. It applies a direct-method procedure to break the phase ambiguity intrinsic to one-wavelength anomalous scattering (OAS) or single isomorphous replacement (SIR) data.

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

Abstract Both 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.

Direct-method structure determination of the native azurin II protein using one-wavelength anomalous scattering data.

The one-wavelength anomalous scattering (OAS) X-ray diffraction data of azurin II, a copper-containing protein from Alcaligenes xylosoxidans were collected at the Photon Factory, Japan at a 'routine' wavelength of 0.97 A. The structure had been originally solved by the molecular-replacement method [Dodd, Hasnain, Abraham, Eady & Smith (1995). Acta Cryst. D51, 1052-1064]. As a technique of ab initio structure determination, the direct method [Fan, Hao, Gu, Qian, Zheng & Ke (1990). Acta Cryst. A46, 935-939] was attempted to break the phase ambiguity intrinsic to OAS data. The phases were then improved using the solvent-flattening method. The final electron-density map clearly shows most Calpha positions and many side chains and it is traceable without prior knowledge of the structure. It is concluded that the direct method is capable of phasing anomalous scattering data collected at one wavelength from moderate-sized native proteins (M(w) approximately 20 kDa) which contain copper or atoms with a similar scattering power.

Combining direct methods with isomorphous replacement or anomalous scattering data. V. Comparison of different phasing methods in the OAS case

Different methods for resolving the phase ambiguity resulting from the OAS (one-wavelength anomalous scattering) technique are compared in the application to two model protein structures. It is concluded that the information from both Sim's and Cochran's distributions is valuable in separating the phase doublets. However, the combination of Sim's and Cochran's distributions can lead to a better result than that obtainable by using either alone.

Combining direct methods with isomorphous replacement or anomalous scattering data. III. The incorporation of partial structure information

The probability formulas given in Parts I and II of this series have been improved by incorporating the information contained in Sim's distribution. Possible applications to the discrimination of the phase ambiguities arising from the single isomorphous replacement technique, the one-wavelength anomalous scattering (OAS) technique or pseudo centrosymmetry in small structures are discussed. With a set of experimental protein OAS data, the efficiency of the improved formula has been shown to be better than that of the older one.

Breaking the phase ambiguities arising from anomalous scattering technique by the direct method – applied to a known protein structure

The method proposed by Fan et al. has been applied to the discrimination of phase doublets arising from the experimental OAS (one-wave-length anomalous scattering) data of the Hg-derivative of APP. Encouraging result was obtained which showed that the method is hopeful to be an important tool in the structure analysis of protein crystals.

Combining direct methods with isomorphous replacement or anomalous scattering data. II. The treatment of errors

The error treatment given by Blow & Crick [Acta Cryst. (1959). 12, 794-802] in the isomorphous replacement method can be readily introduced into direct methods when they are used to handle the single isomorphous replacement (SIR) or the one-wavelength anomalous scattering (OAS) data. The 'best phase relationship' is defined similarly to the 'best Fourier'. Expressions of the 'best phase' and the 'figure of merit' for individual reflection have been derived for the SIR or OAS case. These enable initial signs to be obtained for a set of ΔϕH without knowing the sign of any one ΔϕH in advance. Finally, a weighting scheme is proposed for the refinement of signs and magnitudes of ΔϕH.