Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination

• Published in: Acta crystallographica. Section D, Biological crystallography. Vol. 70; no. 9; pp. 2331 - 2343
• Main Authors: Chen, Chung-De, Huang, Yen-Chieh, Chiang, Hsin-Lin, Hsieh, Yin-Cheng, Guan, Hong-Hsiang, Chuankhayan, Phimonphan, Chen, Chun-Jung
• Format: Journal Article
• Language: English
• Published: 5 Abbey Square, Chester, Cheshire CH1 2HU, England International Union of Crystallography 01.09.2014; Wiley Subscription Services, Inc
• Subjects: ab initio structure determination; Angle of reflection; CHAINS; CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; Construction; CORRELATIONS; Crystallography, X-Ray; DENSITY; direct phase selection; Dispersions; ELECTRON DENSITY; electron-density improvement; ELECTRONS; ERRORS; Mathematical models; MATHEMATICAL SOLUTIONS; MODIFICATIONS; Molecular Structure; MOLECULES; OPTIMIZATION; Phase error; PROTEINS; REFLECTION; Research Papers; SOLUTIONS; WAVELENGTHS; ab initio structure determination; electron-density improvement; direct phase selection
• ISSN: 1399-0047; 0907-4449; 1399-0047
• DOI: 10.1107/S1399004714013868

Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron‐density modification, model building and structure determination of biological macromolecules using the single‐wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ1 and ϕ2) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase‐selection method utilizing the θDS list as a criterion to select optimized phases ϕam from ϕ1 or ϕ2 of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕSAD has been developed. Based on this work, reflections with an angle θDS in the range 35–145° are selected for an optimized improvement, where θDS is the angle between the initial phase ϕSAD and a preliminary density‐modification (DM) phase ϕDMNHL. The results show that utilizing the additional direct phase‐selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron‐density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase‐selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.