Direct Methods Research In Protein Crystallography

The program OASIS which conbines direct methods with conventional protein crystallographic methods has been proved very successful for phasing of portein diffraction data. In this paper, we develop the methods and the program from theory, application and automation, which are included in this paper.1, One of the essential points of the direct-method SAD phasing for proteins is to express the bimodal SAD phase distribution by the sum of two Gaussian functions peaked respectively at?h"+|??h| and?h"-|??h|. The probability for??h being positive (P+) can be derived based on the Cochran distribution in direct methods. Hence the SAD phase ambiguity can be resolved by multiplying the Gaussian function peaked at?h"+|??h.|with P+and multiplying the Gaussian function peaked at?h"-|??h| with P(1P+). Direct-method SAD phasing has been proved powerful in breaking SAD phase ambiguities, in particular when anomalous-scattering signals are weak. However, the approximation of bimodal phase distributions by the sum of two Gaussian functions introduces considerable errors. In this paper we show that a much better approximation can be achieved by replacing the two Gaussian functions with two von Mises distributions. This new method leads to significant improvement of the efficiency of direct-method SAD-phasing.2, In this paper, we create a new mode to Combine SAD/SIR iteration and MR iteration in partial-model extension of proteins. There are two kinds of dual-space partial-model extension which involve the direct-method program OASIS. The first kind, named SAD/SIR iteration uses SAD/SIR information, while the second kind, named MR iteration does not use that information. In general, SAD/SIR iteration is more powerful since more experimental information is used. However, in most cases when protein structures are solved with the molecular replacement method, SAD/SIR information is not available. Thus the MR iteration is particularly useful for the completion of models from molecular replacement. The SAD/SIR iteration will be automatically used in OASIS for data sets containing SAD/SIR signals, while the MR iteration will be dedicated to data sets without SAD/SIR signals. The present paper shows that for data containing SAD/SIR signals, a combination of SAD/SIR iteration and MR iteration could lead to significantly better results than that obtained from the SAD/SIR iteration alone. 3, A new GUI is provided for controlling and real-time monitoring the dual-space iterative process with OASIS4.0, which will be discussed in detail in the present paper.