Book ChapterDOI
SHELXL: high-resolution refinement.
TLDR
The program is designed to be easy to use and general for all space groups and uses a conventional structure-factor calculation rather than a fast Fourier transform (FFT) summation, which is much slower than programs written specifically for macromolecules.Abstract:
Publisher Summary SHELXL-93 was originally written as a replacement for the refinement part of the small-molecule program SHELX-76. The program is designed to be easy to use and general for all space groups and uses a conventional structure-factor calculation rather than a fast Fourier transform (FFT) summation. The latter would be faster but in practice involves some small approximations and is not suitable for the treatment of anomalous dispersion or anisotropic thermal motion. The price to pay for the extra precision and generality is that SHELXL is much slower than programs written specifically for macromolecules. This is compensated for, to some extent, by the better convergence properties, reducing the amount of manual intervention required. A new version, SHELXL-97, was released in May 1997; this is the version described in the chapter. The changes are primarily designed to make the program easier to use for macromolecules. Advances in cryogenic techniques, area detectors, and the use of synchrotron radiation enable macromolecular data to be collected to higher resolution than was previously possible. In practice, this tends to complicate the refinement because it is possible to resolve finer details of the structure. It is often necessary to model alternative conformations, and in a few cases, even anisotropic refinement is justified.read more
Citations
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Journal ArticleDOI
A short history of SHELX
TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
Journal ArticleDOI
Towards automated crystallographic structure refinement with phenix.refine
Pavel V. Afonine,Ralf W. Grosse-Kunstleve,Nathaniel Echols,Jeffrey J. Headd,Nigel W. Moriarty,Marat Mustyakimov,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Peter H. Zwart,Paul D. Adams,Paul D. Adams +11 more
TL;DR: This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
Journal ArticleDOI
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Dorothee Liebschner,Pavel V. Afonine,Matthew L. Baker,Gábor Bunkóczi,Vincent B. Chen,Tristan I. Croll,Bradley J. Hintze,Li-Wei Hung,Swati Jain,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Billy K. Poon,Michael G. Prisant,Randy J. Read,Jane S. Richardson,David S. Richardson,Sammito,Oleg V. Sobolev,Duncan H. Stockwell,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Lizbeth L. Videau,Carmen J. Williams,Paul D. Adams,Paul D. Adams +26 more
TL;DR: Recent developments in the Phenix software package are described in the context of macromolecular structure determination using X-rays, neutrons and electrons.
Journal ArticleDOI
Crystal structure of parallel quadruplexes from human telomeric DNA.
TL;DR: This crystal structure of a quadruplex formed from four consecutive human telomeric DNA repeats and grown at a K+ concentration that approximates its intracellular concentration suggests a straightforward path for telomere folding and unfolding, as well as ways in which it can recognize telomerre-associated proteins.
Journal ArticleDOI
Real-space refinement in PHENIX for cryo-EM and crystallography.
Pavel V. Afonine,Pavel V. Afonine,Billy K. Poon,Randy J. Read,Oleg V. Sobolev,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Paul D. Adams,Paul D. Adams +9 more
TL;DR: In this article, the authors describe the implementation of real-space refinement in the phenixreal_space-refine program from the PHENIX suite, which makes use of extra information such as secondary-structure and rotamer-specific restraints.
References
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Journal ArticleDOI
PROCHECK: a program to check the stereochemical quality of protein structures
TL;DR: The PROCHECK suite of programs as mentioned in this paper provides a detailed check on the stereochemistry of a protein structure and provides an assessment of the overall quality of the structure as compared with well refined structures of the same resolution.
Journal ArticleDOI
Improved methods for building protein models in electron density maps and the location of errors in these models.
TL;DR: In this paper, the authors describe strategies and tools that help to alleviate this problem and simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.
Journal ArticleDOI
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures.
TL;DR: In this article, a statistical quantity (RfreeT) is defined to measure the agreement between observed and computed structure factor amplitudes for a 'test' set of reflections that is omitted in the modelling and refinement process.
Journal ArticleDOI
Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement
Richard A. Engh,Robert Huber +1 more
TL;DR: In this article, a statistical survey of X-ray structures of small compounds from the Cambridge Structural Database is used for the refinement of protein structures determined by X-Ray crystallography.
Journal ArticleDOI
Can X‐ray data distinguish bonding effects from vibrational smearing?
TL;DR: In this article, the success of this separation can be tested by comparison of the vibration ellipsoids of bonded atom pairs, which should have equal amplitudes in the bond direction.
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