Optimizing DREAR and SnB parameters for determining Se-atom substructures.

Abstract

The determination of the anomalous scattering substructure is the first essential step in any successful macromolecular structure determination using the multiwavelength anomalous diffraction (MAD) technique. The diffE method of calculating difference Es in conjunction with SnB has had considerable success in determining large Se-atom substructures. An investigation of the parameters used in both the data-reduction and error-analysis routines (DREAR) as well as the SnB phasing process itself was undertaken to optimize these parameters for more efficient use of the procedure. Two sets of selenomethionyl S-adenosylhomocysteine hydrolase MAD data were used as test data. The elimination of all erroneously large differences prior to phasing was found to be critical and the best results were obtained from accurate highly redundant intensity measurements. The high-resolution data collected in the typical MAD experiment are sufficient, but the inclusion of low-resolution data below 20 A improved the success rate considerably. Although the best results have been obtained from single-wavelength peak anomalous diffraction data alone, independent SnB analysis of data measured at other wavelengths can provide confirmation for questionable sites.