Book ChapterDOI
Processing of X-ray diffraction data collected in oscillation mode
Zbyszek Otwinowski,Wladek Minor +1 more
Reads0
Chats0
TLDR
The methods presented in the chapter have been applied to solve a large variety of problems, from inorganic molecules with 5 A unit cell to rotavirus of 700 A diameters crystallized in 700 × 1000 × 1400 A cell.Abstract:
Publisher Summary X-ray data can be collected with zero-, one-, and two-dimensional detectors, zero-dimensional (single counter) being the simplest and two-dimensional the most efficient in terms of measuring diffracted X-rays in all directions. To analyze the single-crystal diffraction data collected with these detectors, several computer programs have been developed. Two-dimensional detectors and related software are now predominantly used to measure and integrate diffraction from single crystals of biological macromolecules. Macromolecular crystallography is an iterative process. To monitor the progress, the HKL package provides two tools: (1) statistics, both weighted (χ2) and unweighted (R-merge), where the Bayesian reasoning and multicomponent error model helps obtain proper error estimates and (2) visualization of the process, which helps an operator to confirm that the process of data reduction, including the resulting statistics, is correct and allows the evaluation of the problems for which there are no good statistical criteria. Visualization also provides confidence that the point of diminishing returns in data collection and reduction has been reached. At that point, the effort should be directed to solving the structure. The methods presented in the chapter have been applied to solve a large variety of problems, from inorganic molecules with 5 A unit cell to rotavirus of 700 A diameters crystallized in 700 × 1000 × 1400 A cell.read more
Citations
More filters
Journal ArticleDOI
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor
Krzysztof Palczewski,Takashi Kumasaka,Tetsuya Hori,Craig A. Behnke,H. Motoshima,Brian A. Fox,I. Le Trong,David C. Teller,Tetsuji Okada,Ronald E. Stenkamp,Masaki Yamamoto,Masashi Miyano +11 more
TL;DR: This article determined the structure of rhodopsin from diffraction data extending to 2.8 angstroms resolution and found that the highly organized structure in the extracellular region, including a conserved disulfide bridge, forms a basis for the arrangement of the sevenhelix transmembrane motif.
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
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate
Lenny Dang,David W. White,Stefan Gross,Bryson D. Bennett,Mark A. Bittinger,Edward M. Driggers,Valeria Fantin,Hyun Gyung Jang,Shengfang Jin,Marie C. Keenan,Kevin Marks,Robert M. Prins,Patrick S. Ward,Katharine E. Yen,Linda M. Liau,Joshua D. Rabinowitz,Lewis C. Cantley,Craig B. Thompson,Matthew G. Vander Heiden,Matthew G. Vander Heiden,Shinsan M. Su +20 more
TL;DR: It is shown that cancer-associated IDH1 mutations result in a new ability of the enzyme to catalyse the NADPH-dependent reduction of α-ketoglutarate to R(-)-2-hydroxyglutarate (2HG), and that the excess 2HG which accumulates in vivo contributes to the formation and malignant progression of gliomas.
Journal ArticleDOI
Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å.
TL;DR: The crystal structure of photosystem II is reported, finding that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water molecules were bound to the Mn4CaO5 cluster; some of them may therefore serve as substrates for dioxygen formation.
Journal ArticleDOI
Molecular basis of agonism and antagonism in the oestrogen receptor.
Andrzej M. Brzozowski,Ashley C. W. Pike,Zbigniew Dauter,Roderick E. Hubbard,Tomas Bonn,Owe Engström,Lars Öhman,Geoffrey L. Greene,Jan-Åke Gustafsson,Mats Carlquist +9 more
TL;DR: The crystal structures of the LBD of ER in complex with the endogenous oestrogen, 17β-oestradiol, and the selective antagonist raloxifene provide a molecular basis for the distinctive pharmacophore of the ER and its catholic binding properties.
References
More filters
Journal ArticleDOI
An empirical method for correcting diffractometer data for absorption effects
N. Walker,David I. Stuart +1 more
TL;DR: In this article, a Fourier series in the polar angles of the incident and diffracted beam paths is used to model an absorption surface for the difference between the observed and calculated structure factors.
Journal ArticleDOI
Evaluation of Single-Crystal X-ray Diffraction Data from a Position-Sensitive Detector
TL;DR: In this paper, a Fortran program is developed for the reduction of single-crystal diffraction data from a sequence of adjacent rotation pictures recorded at a fixed X-ray wavelength by an electronic area detector.
Patent
Data collection and processing
TL;DR: In this article, a computer system for calculating, and displaying in real time, wages earned by piece workers comprises a plurality of slave data retrieval units, SDRUs (8) which are associated with respective work stations at which workers are working e.g. on sewing machines.
Journal ArticleDOI
Automatic indexing of rotation diffraction patterns
TL;DR: In this article, a method for assigning indices to a set of single-crystal reflections recorded by the rotation-oscillation technique using a fixed X-ray wavelength is described.
Journal ArticleDOI
The use of an imaging proportional counter in macromolecular crystallography
Andrew Howard,Gary L. Gilliland,Barry C. Finzel,Thomas L. Poulos,Douglas H. Ohlendorf,Francis R. Salemme +5 more
TL;DR: A multiwire proportional chamber known as an imaging proportional counter has been used to collect X-ray intensity data for the determination of several structures by molecular replacement or difference Fourier analysis and has provided data for numerous other macromolecular crystallographic projects.