Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement
نویسندگان
چکیده
منابع مشابه
Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement.
Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common use today have been designed on the assumption that each type of bond or angle has a single ideal value that is independent of context. However, recent work has shown that the ideal values are,...
متن کاملA new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream.
Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriarty et al. (2014), FEBS...
متن کاملConformation-dependent restraints for polynucleotides: I. Clustering of the geometry of the phosphodiester group
The refinement of macromolecular structures is usually aided by prior stereochemical knowledge in the form of geometrical restraints. Such restraints are also used for the flexible sugar-phosphate backbones of nucleic acids. However, recent highly accurate structural studies of DNA suggest that the phosphate bond angles may have inadequate description in the existing stereochemical dictionaries...
متن کاملAutomated real-space refinement of protein structures using a realistic backbone move set.
Crystals of many important biological macromolecules diffract to limited resolution, rendering accurate model building and refinement difficult and time-consuming. We present a torsional optimization protocol that is applicable to many such situations and combines Protein Data Bank-based torsional optimization with real-space refinement against the electron density derived from crystallography ...
متن کاملKeep it together: restraints in crystallographic refinement of macromolecule–ligand complexes
A short introduction is provided to the concept of restraints in macromolecular crystallographic refinement. A typical ligand restraint-generation process is then described, covering types of input, the methodology and the mechanics behind the software in general terms, how this has evolved over recent years and what to look for in the output. Finally, the currently available restraint-generati...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: FEBS Journal
سال: 2014
ISSN: 1742-464X
DOI: 10.1111/febs.12860