Biomedical subjects

Rocco Caliandro

Publications and source records attributed to Rocco Caliandro.

4 recordsLinked to original sources

PubMed2005

Ab initio phasing at resolution higher than experimental resolution.

Owing to the limited experimental resolution of data in macromolecular crystallography, ab initio phasing is successful only when atomic or quasi-atomic resolution data are available. It is shown that extrapolating the moduli and phases of non-measured reflections beyond and behind the experimental resolution limit makes the ab initio phasing process more efficient and leads to crystal structure solution even in cases in which the standard SIR2004 program does not succeed. Moreover, use of the extrapolated values improves the quality of the final electron-density maps and makes the recognition of the correct structure among several trial structures easier.

Algorithms↗

PubMed2005

The partial structure with errors: a probabilistic treatment.

The method of the joint probability distribution functions has been applied to the case in which observed (with errors) and calculated structure factors are available, the latter referred to a part of the structure with finite errors in the coordinates, the thermal parameters and the scattering factors. Results obtained by other authors are confirmed and generalized. A new relationship is found to estimate the parameter sigmaA, affecting the reliability of the estimates of cos(varphi-varphip). Some practical applications are described.

Journal Article↗

PubMed2005

Phasing at resolution higher than the experimental resolution.

Limited experimental resolution is a unavoidable feature in macromolecular crystallography: it may hinder or make difficult the determination of the crystal structure. A novel procedure is presented which from an approximate electron-density map extrapolates the moduli and phases of non-measured reflections beyond and behind the experimental resolution limit. Applications to a set of test structures show that the extrapolation can be successfully accomplished. As a consequence, the phase estimates of the observed reflections are subsequently improved and the interpretability of the corresponding electron-density map increases. The use of the extrapolated values for the non-measured reflections provides additional information for the map, which shows a resolution higher than the experimental resolution.

Algorithms↗

PubMed2003

Ab initio protein phasing at 1.4 A resolution: the new phasing approach of SIR2003-N.

New algorithms for solving ab initio protein crystal structures have been identified and implemented in a modified version of the program SIR2002. They succeed in solving numerous protein structures diffracting at atomic resolution; the solution was also attained when data were cut at 1.4 A resolution. The direct-space refinement procedure of SIR2003-N takes advantage of using the envelope of the protein, calculated during the phasing process from the current phases. The electron-density map is modified by assuming different weights for pixels within the envelope or out of it, so tentatively depleting the intensities of the false peaks. The map is then inverted and the resulting phase sets may improve their values. The new phasing strategy is also based on an optimal use of some figures of merit, one of which may be successfully applied in the early stages of the phasing process: only the most promising trials are submitted to the complete phasing procedure, so saving computing time. SIR2003-N has been successfully applied also in solving some protein structures diffracting at 1.4-1.5 A resolution.

Algorithms↗