Phase Improvement

Abstract

After a first set of protein phases is obtained with the isomorphous replacement method, the molecular replacement method, or the multiple wavelength anomalous dispersion method and an electron density map 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 may be in one of the following forms:

• 1. The structure is partially known.

• 2. The protein molecules distinguish themselves as relatively high regions of electron density and their boundaries can be estimated. The electron density between them is then set to a constant value or adjusted otherwise.