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abstracts
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.
abstracts
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.
