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Phasing Procedure (phasing + procedure)
Selected AbstractsApplications of ACORN to data at 1.45 Å resolutionJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2004V. Rajakannan One of the main interests in the molecular biosciences is in understanding structure,function relations and X-ray crystallography plays a major role in this. ACORN can be used as a comprehensive and efficient phasing procedure for the determination of protein structures when atomic resolution data are available. An initial model can automatically be built by ARP/wARP followed by REFMAC for refinement. The , helices and , sheets occurring in many protein structures can be taken as starting fragments for structure solution in ACORN. ACORN, along with ARP/wARP followed by REFMAC, can be an ab initio method for solving protein structure for which data are better than 1.2 Å (atomic resolution). Attempts are here made in extending its applications to real data at 1.45 Å resolution and also to truncated data at 1.6 Å resolution. Two previously known structures, congerin II and alkaline cellulase N257, were resolved using the above approach. Automatic structure solution, phasing and refinement for real data at still lower resolutions for proteins of various complexities are being carried out. Data mining of the secondary structural features using PDB is being carried out for this new approach for `seed-phasing' to ACORN. [source] MAD techniques applied to powder data: finding the structure given the substructureACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2009Angela Altomare The joint probability distribution function method is applied to multiple-wavelength anomalous dispersion (MAD) powder data. The distributions are calculated by assuming prior knowledge of the scattering intensities at two wavelengths and of the anomalous-scatterer substructure. The method leads to formulas estimating the full structure phases and their reliability. The procedure has been applied to two structures, one unknown and one known; the second was used as a control for the phasing procedure. In spite of the unavoidable peak overlapping in the diffraction pattern, the formulas proved to be very effective. Combined with a new algorithm for phase extension, they enabled the solution of both crystal structures. [source] Phasing possibilities using different wavelengths with a xenon derivativeJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2002Santosh Panjikar Xenon derivatives are generally expected to be isomorphous with the native; however, the K - and L -absorption edges are not easily accessible on most synchrotron beamlines, which might limit their usefulness in phase determination. Various phasing procedures for xenon-derivatized porcine pancreatic elastase have been investigated using data sets measured at three generally accessible wavelengths. The importance of highly redundant data in measuring precise anomalous differences is highlighted and it is shown that, after such measurements, a single isomorphous replacement anomalous scattering (SIRAS) procedure yields a better phase set than those generated by single anomalous scattering (SAS) or multiwavelength anomalous diffraction (MAD) procedures. [source] Diffraction data analysis in the presence of radiation damageACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Dominika Borek In macromolecular crystallography, the acquisition of a complete set of diffraction intensities typically involves a high cumulative dose of X-ray radiation. In the process of data acquisition, the irradiated crystal lattice undergoes a broad range of chemical and physical changes. These result in the gradual decay of diffraction intensities, accompanied by changes in the macroscopic organization of crystal lattice order and by localized changes in electron density that, owing to complex radiation chemistry, are specific for a particular macromolecule. The decay of diffraction intensities is a well defined physical process that is fully correctable during scaling and merging analysis and therefore, while limiting the amount of diffraction, it has no other impact on phasing procedures. Specific chemical changes, which are variable even between different crystal forms of the same macromolecule, are more difficult to predict, describe and correct in data. Appearing during the process of data collection, they result in gradual changes in structure factors and therefore have profound consequences in phasing procedures. Examples of various combinations of radiation-induced changes are presented and various considerations pertinent to the determination of the best strategies for handling diffraction data analysis in representative situations are discussed. [source] | ||||||||||