Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density andab initiostructure determination

Abstract

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 (ϕ1and 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 θDSlist as a criterion to select optimized phases ϕamfrom ϕ1or ϕ2of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕSADhas been developed. Based on this work, reflections with an angle θDSin the range 35–145° are selected for an optimized improvement, where θDSis the angle between the initial phase ϕSADand 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 asRESOLVEorDMfromCCP4, 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.