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Acta Cryst. (2014). A70, C319
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In translational noncrystallographic symmetry (tNCS), two or more copies of a component are present in a similar orientation in the asymmetric unit of the crystal. This causes systematic modulations of the intensities in the diffraction pattern, leading to problems with methods that assume, either implicitly or explicitly, that the distribution of intensities is a function only of resolution. To characterize the statistical effects of tNCS accurately, it is necessary to determine the translation relating the copies, any small rotational differences in their orientations, and the size of random coordinate differences caused by conformational differences. An algorithm has been developed to estimate these parameters and refine their values against a likelihood function. By accounting for the statistical effects of tNCS, it is possible to unmask the competing statistical effects of twinning and tNCS and to more robustly assess the crystal for the presence of twinning. Modified likelihood functions that account for the statistical effects of tNCS have been developed for use in molecular replacement and implemented in Phaser. With the use of these new targets, it is now possible to solve structures that eluded earlier versions of the program. Pseudosymmetry and space group ambiguities often accompany tNCS, but the new version of Phaser is less likely to fall into the traps that these set.

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Acta Cryst. (2014). A70, C327
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Although macromolecular crystallography has been greatly accelerated by the development of automated software for data processing, phasing, and model building, most structures require significant manual intervention to yield a truly final model. In addition to missing individual protein or nucleic residues, this may include the addition of alternate conformations, ligands (both free and covalently bound), elemental ions, or modified amino acids. We have developed a number of tools to streamline several of these steps within the Phenix software suite (Adams et al. 2010): 1) an automated pipeline for the determination of ligand-bound structures by molecular replacement (Echols et al. 2014a); 2) placement of elemental ions during refinement (Echols et al. 2014b), as an extension of solvent placement; 3) fitting of additional conformations of protein residues into difference density. These tools reliably reproduce published structures in a majority of test cases, and in several instances identify details omitted by the original authors. Their low false positive rate makes them suitable for use in high-throughput workflows.

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Acta Cryst. (2014). A70, C493
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"The Structural Biology Knowledgebase (SBKB, http://sbkb.org) was established as a data aggregator to facilitate research design and analysis for a wide variety of biological systems. It serves as a single resource that integrates structure, sequence, and functional annotations plus technical information regarding protein production and structure determination. Researchers can search the SBKB by sequence, PDB ID or UniProt accession code, and receive an up-to-the-minute list of matching 3D experimental structures from the Protein Data Bank, pre-built theoretical models from the Protein Model Portal, annotations from 100+ open biological resources, structural genomics target histories and protocols from TargetTrack, and ready-to-use DNA clones from DNASU. It also possible to find structures according to functional relevance (KB-Rank tool), or find related technologies and publications from the PSI Technology and Publications Portals, respectively. Interactive tools such as real-time theoretical modeling and biophysical parameter prediction also enhance understanding of proteins that are not yet well characterized. Experimentally-focused ""hubs"" collect links to helpful tools and resources for the areas of Structural Targets; Structure, Sequence and Function; Homology Models, Methods and Technologies, and Membrane Proteins. In partnership with the Nature Publishing Group, latest research highlights and articles on specific biological systems are written monthly to share the impact of structural biology. This presentation will demonstrate how the SBKB turns data into knowledge and enables further research. SBKB is funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health (U01 GM093324)."

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Acta Cryst. (2014). A70, C782
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Refinement of macromolecular structures against low-resolution crystallographic data is limited by the ability of current methods to arrive at a high-quality structure with realistic geometry. We have developed a new method for crystallographic refinement which combines the Rosetta sampling methodology and all atom energy function with likelihood-based reciprocal space refinement in Phenix, and find, on a test set of difficult low-resolution refinement cases, that models refined with the new method have significantly improved model geometry, and in most cases, lower free R factors and RMS deviation to the final model. Integration of the software packages additionally makes advanced sampling methods used in structure prediction and design available for crystallographic refinement and model-building, and also provides a strategy for improving the Rosetta force field for better agreement with experimental data.
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