Accelerating structural biology with phaser crystallographic software. Read, journaljournal of applied crystallography, year 2007, volume40, pages658 674. Crystallographic characterization of ccg repeats nucleic. Phaser crystallographic software university of cambridge. Journal of applied crystallography wiley online library. Phaser calculates correction factors for the expected intensities in the presence of translational non crystallographic symmetry tncs, and is able to solve structures with complex patterns of tncs. Introduction improved crystallographic methods rely on both improved automation and improved algorithms. This area of crystallography is continually expanding and evolving, and the introduction of new methods that use the latest technology is. At the tail end of last year i bought a 2007 4x4 supercrew f150 to serve as my daily driver. At their cores, photosystems i and ii contain a heterodimeric reaction center. Combining sophisticated algorithms and automated rapid search calculations, phaser solves structures.
Automated crystallographic structure solution in phenix. This software can be useful for the development of improved phasing methods and their release, including source code, to the crystallographic community. Articles published in journal of applied crystallography focus on these methods and their use in identifying structural and diffusioncontrolled phase transformations. Institute of bioorganic chemistry, polish academy of sciences, noskowskiego 1214, 61704 poznan, poland.
Solution and crystal structures of a cterminal fragment of the neuronal isoform of the polypyrimidine tract binding protein nptb. Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. Randy read in cambridge, uk, was first released in 2003, and has now been incorporated into two major crystallographic software packages, ccp4 and phenix. Improved molecular replacement by density and energyguided protein structure optimization. Phaser a stunning method for solving crystal structures. Phaser crystallographic software, journal of applied. Mccoy aj, grossekunstleve rw, adams pd, winn md, storoni. Crystallographic approaches to study the interaction modes.
Laurent c storonis research while affiliated with university of cambridge and other places. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community. I was well aware of the cam phaser issues that fords 3v engine can have. If a class has an entry in the via column it means you can quickly access it through a local reference. It has been developed by randy reads group at the university of cambridge and will be available through the phenix and ccp4 software suites, and directly from this site. In plants, algae, and cyanobacteria, large molecular complexesphotosystems i and iiconvert light energy into chemical energy, releasing oxygen as a byproduct. These tools are available in the right hand side of the main phenix gui window, filed under their respective.
Many research topics in condensed matter research, materials science and the life sciences make use of crystallographic methods to study crystalline and noncrystalline matter with neutrons, xrays and electrons. At the pharma giant, astrazeneca, phaser is considered the tool of choice for solving structures by mr. H37rv genome and inserted into the expression vector pmcsg7 1. Mccoy aj, grosse kunstleve rw, adams pd, winn md, storoni lc, read rj. Randy read cambridge institute for medical research.
Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and. Professor read is known internationally for his outstanding and fundamental contributions to the development of macromolecular crystallographic software. Recombinant protein with an nterminal 6xhis tag was overexpressed in. Phaser is a program for phasing macromolecular crystal structures by both molecular. The novel phasing algorithms implemented in phaser have been. This section only covers features unique to sad phasing, including instructions for mrsad. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct. Crystallographic data are available in the rcsb pdb with the identifiers 6ir4 for biou in the resting state p3 1 21, 6k36 for the bioudan conjugate p3 1. Synopsis phaser description molecular replacement, sad phasing, anisotropy correction, cell content analysis, translational ncstwin analysis, gyration refinement, pruning, single atom mr, and sceds substructure determinationnormal mode perturbation of pdb. The threedimensional structures of large biomolecules important in the function and mechanistic pathways of all living systems and viruses can be determined by xray diffraction from crystals of these molecules and their complexes. Phaser is a program for phasing macromolecular crystal structures with maximum. However, the use of phaser in the presence of tncs requires the nature of the tncs to be understood by the user. Frequently asked questions about molecular replacement. The automated molecular replacement method in phaser involves several discrete steps anisotropy correction.
Phaser crystallographic software mccoy 2007 journal of applied crystallography wiley online library. It has been developed by randy reads group at the cambridge institute for medical research cimr in the university of cambridge and is available through the phenix and ccp4 software suites. The phaser crystallographic software, developed by read and colleagues. Mccoy aj, grossekunstleve rw, adams pd, winn md, storoni lc, read rj. The novel phasing algorithms implemented in phaser have been developed using maximum likelihood. Crystallographic characterization of ccg repeats agnieszka kiliszek. It demonstrates a two component search through using the tem1 beta lactamasebetalactamase inhibitor complex example. Phaser crystallographic software mccoy 2007 journal. Richard mifsud explains how to use phaser mr from the phenix gui.
The journal is the primary place where crystallographic computer program information is published. The structure of the icr ecd antiicr ecd fv complex is determined by molecular replacement with the program mr phaser mccoy et al. Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. Insights into hunter syndrome from the structure of iduronate2sulfatase. The phaser crystallographic software, developed by read and colleagues, implements powerful new likelihoodbased methods for mr and sad phasing and has made a large impact, accelerating over the period 200820. Its algorithms are based on maximum likelihood probability theory and multivariate statistics. Read use a different maximum likelihood function for its rfn which is scored in terms of log likelihood gain llg and resists direct comparison with. Supplementary information, data s1 nature research.
The novel phasing algorithms implemented in phaser have been developed using maximum likelihood and multivariate statistics. Phaser crystallographic software phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. The iucr is a scientific union serving the interests of crystallographers and other scientists employing crystallographic methods. Phaser is a program for phasing macromolecular crystal structures. The energybased refinement of lowresolution protein structure models to atomiclevel accuracy is a major challenge for computational structural biology. Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Journal of applied crystallography 40 4, 658674, 2007. Phaser is a program that aims to facilitate automation of phasing methods. A suicide enzyme catalyzes multiple reactions for biotin.
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