Journal•ISSN: 1574-8707
International Tables for Crystallography
About: International Tables for Crystallography is an academic journal. The journal publishes majorly in the area(s): Scattering & Wyckoff positions. Over the lifetime, 227 publications have been published receiving 10939 citations.
Topics: Scattering, Wyckoff positions, Diffraction, Crystallographic Information File, Diffraction topography
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TL;DR: PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures.
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
Keywords:
PHENIX;
Python;
algorithms
9,732 citations
TL;DR: MolProbity is the authors’ contribution to helping solve the problem of local errors in X-ray crystallography and this chapter reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.
Abstract: MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized H-atom placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors’ contribution to helping solve this problem and this chapter reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.
Keywords:
all-atom contacts;
clashscore;
automated correction;
KiNG;
MolProbity;
ribose pucker;
Ramachandran plots;
side-chain rotamers;
model quality;
systematic errors;
database improvement
1,201 citations
TL;DR: autoindexing determines the unit-cell parameters and the orientation of the crystal and integrates the images, which consists of predicting the positions of the Bragg reflections on each image and obtaining an estimate of the intensity of each reflection and its uncertainty.
Abstract: In this chapter the integration of macromolecular diffraction data from two-dimensional area detectors is described. Data integration refers to the process of obtaining estimates of diffracted intensities (and their standard deviations) from the raw images recorded by an X-ray detector. When collecting data, a decision has to be taken about the magnitude of the angular rotation of the crystal during the recording of each image: the rotation per image can be comparable to, or greater than, the angular reflection range of a typical reflection (coarse ϕ slicing), or it can be much less than the reflection width (fine ϕ slicing). The latter approach allows the use of three-dimensional profile fitting and, providing that the detector is relatively noise-free, improves the quality of the resulting data by minimizing the contribution of the X-ray background to the total measured intensity. Methods of integration are described and integration by simple summation and by profile fitting is discussed.
Keywords:
background;
data integration;
detector overloads;
errors;
integration of diffraction data;
outliers;
overloads;
partially recorded reflections;
profile fitting;
standard profiles;
summation integration
721 citations
TL;DR: The structure-validation program PROCHECK is described, which automates the very labor-intensive and therefore time-heavy and expensive process of manually cataloging and verifying the structure of a model.
Abstract: The structure-validation program PROCHECK is described.
Keywords:
PROCHECK;
structure validation
219 citations
TL;DR: Mean bond lengths for organic compounds, derived from the Cambridge Structural Database, are tabulated for 625 different bond types involving the elements C, H, N, O, B, F, P, S, Cl, As, Se, Br, Te and I Associated statistical information characterizes each of the distributions, which are derived from both X-ray and neutron diffraction data as discussed by the authors.
Abstract: Mean bond lengths for organic compounds, derived from the Cambridge Structural Database, are tabulated for 625 different bond types involving the elements C, H, N, O, B, F, P, S, Cl, As, Se, Br, Te and I Associated statistical information characterizes each of the distributions, which are derived from both X-ray and neutron diffraction data
170 citations