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Macromolecular Crystal Structures (macromolecular + crystal_structure)
Selected AbstractsCase-controlled structure validationACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2009Randy J. Read Although many factors influence the quality of a macromolecular crystal structure, validation criteria are usually only calibrated using one of these factors, the resolution. For many purposes this is sufficient, but there are times when one wishes to compare one set of structures with another and the comparison may be invalidated by systematic differences between the sets in factors other than resolution. This problem can be circumvented by borrowing from medicine the idea of the case-matched control: each structure of interest is matched with a control structure that has similar values for all relevant factors considered in this study. In addition to resolution, these include the size of the structure (as measured by the volume of the asymmetric unit) and the year of deposition. This approach has been applied to address two questions: whether structures from structural genomics efforts reach the same level of quality as structures from traditional sources and whether the impact factor of the journal in which a structure is published correlates with structure quality. In both cases, once factors influencing quality have been controlled in the comparison, there is little evidence for a systematic difference in quality. [source] What happens when the signs of anomalous differences or the handedness of substructure are inverted?ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2007Jiawei Wang Proper solution of a macromolecular crystal structure based on anomalous scattering and/or isomorphous differences requires that the anomalous differences in reflection amplitudes be measured properly and that the correct enantiomer of the substructure be selected. If this information is wrong then the resulting electron-density maps will not show the correct structural features, but the reflection phases and map features will be related to the correct ones in a specific way. This text aims to explain how misinterpretation of the Bijvoet differences or of the substructure affects the resulting phases and electron-density maps. [source] Ultrahigh-resolution crystallography and related electron density and electrostatic properties in proteinsJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2008Claude Lecomte With an increasing number of biological macromolecular crystal structures measured at ultrahigh resolution (1,Å or better), it is necessary to extend to large systems the experimental valence electron density modelling that is applied to small molecules. A database of average multipole populations has been built, describing the electron density of chemical groups in all 20 amino acids found in proteins. It allows calculation of atomic aspherical scattering factors, which are the starting point for refinement of the protein electron density, using the MoPro software. It is shown that the use of non-spherical scattering factors has a major impact on crystallographic statistics and results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. It is also possible to obtain a realistic valence electron density model, which is used in the calculation of the electrostatic potential and energetic properties of proteins. [source] On vital aid: the why, what and how of validationACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2009Gerard J. Kleywegt Limitations to the data and subjectivity in the structure-determination process may cause errors in macromolecular crystal structures. Appropriate validation techniques may be used to reveal problems in structures, ideally before they are analysed, published or deposited. Additionally, such techniques may be used a posteriori to assess the (relative) merits of a model by potential users. Weak validation methods and statistics assess how well a model reproduces the information that was used in its construction (i.e. experimental data and prior knowledge). Strong methods and statistics, on the other hand, test how well a model predicts data or information that were not used in the structure-determination process. These may be data that were excluded from the process on purpose, general knowledge about macromolecular structure, information about the biological role and biochemical activity of the molecule under study or its mutants or complexes and predictions that are based on the model and that can be tested experimentally. [source] MIR phasing using merohedrally twinned crystalsACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2003Anke C. Terwisscha van Scheltinga Merohedral twinning is a crystal-growth disorder that seriously hinders the determination of macromolecular crystal structures by isomorphous replacement. The strategies used in the structures solved so far are discussed. Several methods can be used to determine the extent of twinning, the twin fraction and to detwin the data. Accurate determination of the twin fraction by analysing heavy-atom refinement statistics is possible, but only influences the resulting phases slightly. It seems more crucial to restrict the variation in twin fractions between data sets, either by making the twin fractions of some data sets artificially higher or by screening crystals to obtain data with a low twin fraction. [source] | ||||||||||