Locating heavy atoms by integrating direct methods and SIR techniques

Abstract

Direct methods have been applied to the SIR (single isomorphous replacement) case to estimate structure-factor moduli from diffraction magnitudes. The joint probability distribution function P(E(H),E(p),E(d)) has been calculated by explicitly considering, as an additional primitive random variable, the cumulative error arising from measurements and from lack of isomorphism. The specific feature of the approach is that it provides estimated values of |E(H)| which depend on the experimental diffraction data as well as on errors. Some test structures have been used to check the efficiency of the new estimates. Patterson techniques, using the estimated |E(H)|(2) values as coefficients, as well as a tangent procedure, have been implemented into a computer program to locate the heavy atoms automatically. All the experimental tests show that the new approach provides results highly competitive with the traditional |E(H)|(2) estimates.

SIR2011: a new package for crystal structure determination and refinement

“…When SIR-MIR or SAD-MAD (SIRAS-MIRAS) data are available, the first step of the phasing procedure aims at determining the substructure of the heavy or of the anomalously scattering atoms, respectively. The experimental isomorphous data are used to derive, via probabilistic methods (Giacovazzo, Moustiakimov et al, 2004;Burla, Carrozzini, Cascarano, Giacovazzo, Polidori & Siliqi, 2002;Burla et al, 2003Burla et al, , 2004, the most likely values of the normalized structure factor moduli of the heavy or anomalously scattering structure. This is then identified via Patterson techniques, similar to those described in x2.1.…”

Phase improvementviathePhantom Derivativetechnique: ancils that are related to the target structure

“…In accordance with Paper I, the main difficulty for the success of PhD is the fact that |F d | cannot be measured: indeed, d is an unreal structure for which the isomorphism concept is no longer valid, and therefore the well established probabilistic methods (Bragg & Perutz, 1954;Green et al, 1954;Blow & Crick, 1959;Terwilliger & Eisenberg, 1983;Giacovazzo & Siliqi, 2002;Pannu et al, 2003;Giacovazzo et al, 2004) that are valid for isomorphous replacement cannot be directly applied. It may then be useful to identify ancil structures for which the derivative amplitudes |F d | may be carefully estimated.…”