Phase Improvement

Abstract

After a first set of protein phases is obtained using the isomorphous replacement method, the molecular replacement method, or the single- or multiple-wavelength anomalous diffraction method and an electron density map is calculated, the next step is the interpretation of the map in terms of the polypeptide chain. If this is successful and the major part of the chain can, indeed, be followed in the electron density map, refinement of the structure can begin. However, insufficient quality of the electron density map might hamper a complete and unambiguous tracing of the polypeptide chain, increasing the risk of introducing errors in the model, which cannot be easily removed during refinement. In such a case, refinement should be preceded by a process to improve the quality of the map through improvement of the protein phase angles (Podjarny et al., 1987). During phase improvement, all available information on the structure should be used (Brünger and Nilges, 1993). This information might be in one of the following forms: