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Benedetta Carrozzini

Publications and source records attributed to Benedetta Carrozzini.

10 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

Separated and aligned molecular fibres in solid state self-assemblies of cyclodextrin [2]rotaxanes.

The conformations of two [2]rotaxanes, each comprising alpha-cyclodextrin as the rotor, a stilbene as the axle and 2,4,6-trinitrophenyl substituents as the capping groups, have been examined in solution and in the solid state, using (1)H NMR spectroscopy and X-ray crystallography, respectively. In solution, introducing substituents onto the stilbene prevents the cyclodextrin from being localized over one end of the axle. Instead the cyclodextrin moves back and forth along the substituted stilbene. In the solid state, the axles of the rotaxanes form extended molecular fibres that are separated from each other and aligned along a single axis. The molecular fibres are strikingly similar to those formed by the axle component of one of the rotaxanes in the absence of the cyclodextrin, but in the latter case they are neither separated nor all aligned.

Crystallography, X-Ray↗
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↗
PubMed2003

Ab initio protein phasing at 1.4 A resolution.

All the techniques today available for the ab initio crystal structure solution of proteins require that the atomicity condition is satisfied. Accordingly, diffraction data at resolution equal or better than 1.2 A are necessary. This condition reduces the role of the ab initio techniques in macromolecular crystallography. The computer program SIR2002 has been modified in such a way that it may succeed also with 1.4 A resolution diffraction data. The modifications concern all the modules of the program: the modified program also benefits by the efficiency of a figure of merit.

Collagen↗
PubMed2003

SAD or MAD phasing: location of the anomalous scatterers.

The method of joint probability distribution functions is applied in order to estimate the structure-factor moduli of the anomalous scatterer substructure both in the SAD (single-wavelength anomalous dispersion) and in the MAD (multi-wavelength anomalous dispersion) cases. The experimental data |F(1)(+)|, |F(1)(-)|, ..., |F(n)(+)|, |F(n)(-)| measured at n wavelengths are used simultaneously to estimate the value of |F(oa)| arising from the normal scattering of the anomalous scatterers. A practical procedure is described that, when applied to the experimental diffraction data of several proteins, shows robustness and efficiency.

Algorithms↗
PubMed2002

MAD phasing: probabilistic estimate of [F (oa)].

The method of the joint probability distribution function is applied in order to estimate the structure-factor moduli of the anomalous scatterer substructure. The two-wavelength case is examined: the prior knowledge of the moduli [F(1)(+)], [F(1)(-)], [F(2)(+)], [F(2)(-)] is used to predict the value of [F(oa)] arising from the normal scattering of the anomalous scatterers. The conclusive formula is applied to ideal and to real cases: evidence of the usefulness of the approach is obtained.

Computational Biology↗