Likelihood methods with protein powder diffraction data

Time-dependent analysis of K2PtBr6binding to lysozyme studied by protein powder and single crystal X-ray analysis

“…With multiple powder pattern analysis we have then extracted individual reflection intensities using the Pawley method [8] and software PRODD [9,10] and thus been able to show the presence of PtBr 6 2À bound in lysozyme in (Fo À Fc) Fourier omit maps, based on calculated phases from the PDB model 1LZ8, at two binding sites (Fig. 1a, which is a close up of binding site 1).…”

Powder crystallography on macromolecules

“…In one of our most recent studies of the second SH3 domain of ponsin (Margiolaki, Wright, Wilmanns et al, 2007), we exploited radiation-induced anisotropic lattice strains in a specially modified multi-pattern Pawley refinement taking into consideration likelihood criteria for partitioning overlapped peaks (Wright, Markvardsen & Margiolaki, 2007). The outcome of this analysis was a set of improved extracted intensities, in excellent agreement with single-crystal intensities later obtained by an independent experiment.…”

“…In our own laboratory, we have been able to successfully use the MOLREP software (Vagin & Teplyakov, 1997) together with powder data for a variety of small proteins. Integrated intensities are extracted (Wright, 2004) from the powder profile and then treated as if they came from a single crystal, ignoring the overlap problem. Fortunately, the molecular replacement method tolerates errors in the input data as if they were due to errors in the model for the structure.…”

“…In order to benefit from anisotropic changes in unit-cell parameters for intensity extractions, the PRODD refinement program (Wright & Forsyth, 2000;Wright, 2004) was modified to allow a different set of unit-cell parameters to be used for each pattern in a multi-pattern Pawley fit (Pawley, 1981) single list of Bragg-peak intensities are fitted to the profiles while an overall isotropic thermal factor and scale factor for each profile accounts for the bulk of the differences between the patterns. A Pawley refinement of myoglobin using highresolution synchrotron data ( = 0.413465 Å , BM16, ESRF) and the PRODD software illustrated the applicability of the method in cases of significant complexity and severe peak overlap (Wright, 2004).…”

“…In order to benefit from anisotropic changes in unit-cell parameters for intensity extractions, the PRODD refinement program (Wright & Forsyth, 2000;Wright, 2004) was modified to allow a different set of unit-cell parameters to be used for each pattern in a multi-pattern Pawley fit (Pawley, 1981). single list of Bragg-peak intensities are fitted to the profiles while an overall isotropic thermal factor and scale factor for each profile accounts for the bulk of the differences between the patterns.…”