Cluster analysis for phasing with molecular replacement: a feasibility study

Molecular replacement with the simultaneous use of several search functions may solve the phase problem when the conventional molecular-replacement procedure fails to identify the solution

py_convrot : rotation conventions, to understand and to apply

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A program to analyze the distributions of unmeasured reflections

Crystallographic Fourier maps may contain barely interpretable or non-interpretable regions if these maps are calculated with an incomplete set of diffraction data. Even a small percentage of missing data may be crucial if these data are distributed non-uniformly and form connected regions of reciprocal space. Significant time and effort can be lost trying to interpret poor maps, in improving them by phase refinement or in fighting against artefacts, whilst the problem could in fact be solved by completing the data set. To characterize the distribution of missing reflections, several types of diagrams have been suggested in addition to the usual plots of completeness in resolution shells and cumulative data completeness. A computer program, FOBSCOM, has been developed to analyze the spatial distribution of unmeasured diffraction data, to search for connected regions of unmeasured reflections and to obtain numeric characteristics of these regions. By performing this analysis, the program could help to save time during structure solution for a number of projects. It can also provide information about a possible overestimation of the map quality and model-biased features when calculated values are used to replace unmeasured data

Patterson-guided ab initio analysis of structures with helical symmetry.

International audiencePatterson maps, which have a peak for intermolecular vectors between two molecules linked by a pseudo-translation, are widely used for structure solution. However, these maps may contain other peaks that indicate additional important information. In particular, if a molecule has internal symmetry, the Patterson maps may have a peak even when the relation between two molecules is other than a pure translation. A special and frequent case is a crystal that consists of molecules with pseudo-helical symmetry, like RNA or DNA, packed more or less parallel to each other. For such pairs of molecules, the Patterson peak does not simply link the molecular centres but is shifted along the helical axis. The shift is proportional to the rotation between the two molecules. The known step of the helix may be sufficient to obtain a system of linear equations whose solution gives an approximate position for the molecule. This technique may provide crucial information when molecular replacement fails to find a solution or suggests a number of candidates. Instead of repeating numerous molecular-replacement trials varying the model, a model may be positioned directly in place and be modified and refined directly. This Patterson-based search for molecular position has been tested with several solved crystals and has assisted in structure solution of RNA duplexes containing Homo sapiens cytoplasmic or mitochondrial ribosomal decoding sites (A sites)

台灣土壤溫度和熱擴散係數之季節變化

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Acta Crystallogr D Biol Crystallogr

In macromolecular X-ray crystallography, diffraction data sets are traditionally characterized by the highest resolution dhigh of the reflections that they contain. This measure is sensitive to individual reflections and does not refer to the eventual data incompleteness and anisotropy; it therefore does not describe the data well. A physically relevant and robust measure that provides a universal way to define the `actual' effective resolution deff of a data set is introduced. This measure is based on the accurate calculation of the minimum distance between two immobile point scatterers resolved as separate peaks in the Fourier map calculated with a given set of reflections. This measure is applicable to any data set, whether complete or incomplete. It also allows characterizion of the anisotropy of diffraction data sets in which deff strongly depends on the direction. Describing mathematical objects, the effective resolution deff characterizes the `geometry' of the set of measured reflections and is irrelevant to the diffraction intensities. At the same time, the diffraction intensities reflect the composition of the structure from physical entities: the atoms. The minimum distance for the atoms typical of a given structure is a measure that is different from and complementary to deff; it is also a characteristic that is complementary to conventional measures of the data-set quality. Following the previously introduced terms, this value is called the optical resolution, dopt. The optical resolution as defined here describes the separation of the atomic images in the `ideal' crystallographic Fourier map that would be calculated if the exact phases were known. The effective and optical resolution, as formally introduced in this work, are of general interest, giving a common `ruler' for all kinds of crystallographic diffraction data sets

Ab initio phasing based on topological restraints: automated determination of the space group and the number of molecules in the unit cell

International audienceThe connectivity-based phasing method has been demonstrated to be capable of finding molecular packing and envelopes even for difficult cases of structure determination, as well as of identifying, in favorable cases, secondary-structure elements of protein molecules in the crystal. This method uses a single set of structure factor magnitudes and general topological features of a crystallographic image of the macromolecule under study. This information is expressed through a number of parameters. Most of these parameters are easy to estimate, and the results of phasing are practically independent of these parameters when they are chosen within reasonable limits. By contrast, the correct choice for such parameters as the expected number of connected regions in the unit cell is sometimes ambiguous. To study these dependencies, numerous tests were performed with simulated data, experimental data and mixed data sets, where several reflections missed in the experiment were completed by computed data. This paper demonstrates that the procedure is able to control this choice automatically and helps in difficult cases to identify the correct number of molecules in the asymmetric unit. In addition, the procedure behaves abnormally if the space group is defined incorrectly and therefore may distinguish between the rotation and screw axes even when high-resolution data are not available