J. Appl. Cryst.の発刊に際して
10 Mar 1970-Vol. 12, Iss: 1, pp 1-1
About: The article was published on 1970-03-10 and is currently open access. It has received 8159 citations till now.
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TL;DR: Hummingbird is an open-source scalable Python-based software tool for real-time analysis of diffraction data with the purpose of giving users immediate feedback during their experiments.
Abstract: Advances in X-ray detectors and increases in the brightness of X-ray sources combined with more efficient sample delivery techniques have brought about tremendous increases in the speed of data collection in diffraction experiments. Using X-ray free-electron lasers such as the Linac Coherent Light Source (LCLS), more than 100 diffraction patterns can be collected in a second. These high data rates are invaluable for flash X-ray imaging (FXI), where aerosolized samples are exposed to the X-ray beam and the resulting diffraction patterns are used to reconstruct a three-dimensional image of the sample. Such experiments require immediate feedback on the quality of the data collected to adjust or validate experimental parameters, such as aerosol injector settings, beamline geometry or sample composition. The scarcity of available beamtime at the laser facilities makes any delay extremely costly. This paper presents Hummingbird, an open-source scalable Python-based software tool for real-time analysis of diffraction data with the purpose of giving users immediate feedback during their experiments. Hummingbird provides a fast, flexible and easy-to-use framework. It has already proven to be of great value in numerous FXI experiments at the LCLS.
34 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...Hummingbird provides a fast, flexible and easy-to-use framework....
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...The current release of Hummingbird includes a collection of analysis modules for tasks such as detector correction, hit finding (Barty et al., 2014), size and multiple-hit filtering (Hantke et al., 2014), and scanning transmission X-ray microscopy analysis (for scanning experiments)....
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...The analysis modules are built upon Numpy (Jones et al., 2001) and Scipy (van der Walt et al., 2011)....
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...Similar projects like Cheetah (a comprehensive data reduction and analysis tool for diffraction data written in C/C++; Barty et al., 2014), CASS (a data analysis and visualization tool developed for XFEL experiments; Foucar et al., 2012), cctbx.xfel [a Python-based data processing tool for serial femtosecond crystallography (SFX); Sauter et al., 2013] and OnDA (a real-time monitoring tool mainly developed for the needs of SFX; Mariani, 2016) show the need for robust and fast data analysis tools able to cope with the large stream of data produced with XFELs....
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...Similar projects like Cheetah (a comprehensive data reduction and analysis tool for diffraction data written in C/C++; Barty et al., 2014), CASS (a data analysis and visualization tool developed for XFEL experiments; Foucar et al., 2012), cctbx.xfel [a Python-based data processing tool for serial…...
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TL;DR: The crystal structure of a novel MACPF protein, which may play a role in the adaptation of commensal bacteria to host environments in the human gut, was determined and analyzed.
Abstract: Membrane-attack complex/perforin (MACPF) proteins are transmembrane pore-forming proteins that are important in both human immunity and the virulence of pathogens. Bacterial MACPFs are found in diverse bacterial species, including most human gut-associated Bacteroides species. The crystal structure of a bacterial MACPF-domain-containing protein BT_3439 (Bth-MACPF) from B. thetaiotaomicron, a predominant member of the mammalian intestinal microbiota, has been determined. Bth-MACPF contains a membrane-attack complex/perforin (MACPF) domain and two novel C-terminal domains that resemble ribonuclease H and interleukin 8, respectively. The entire protein adopts a flat crescent shape, characteristic of other MACPF proteins, that may be important for oligomerization. This Bth-MACPF structure provides new features and insights not observed in two previous MACPF structures. Genomic context analysis infers that Bth-MACPF may be involved in a novel protein-transport or nutrient-uptake system, suggesting an important role for these MACPF proteins, which were likely to have been inherited from eukaryotes via horizontal gene transfer, in the adaptation of commensal bacteria to the host environment.
34 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Initial screening for diffraction was carried out using the Stanford Automated Mounting system (SAM; Cohen et al., 2002) at the Stanford Synchrotron Radiation Lightsource (SSRL, Menlo Park, California, USA)....
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04 Jan 2010
TL;DR: This paper presents a novel sequence-independent method of aligning protein structures using three-dimensional spherical polar Fourier representations of protein shape using a simple rotationally-invariant pre-filter in tandem with a more sensitive rotational search with little or no reduction in accuracy.
Abstract: This paper presents a novel sequence-independent method of aligning protein structures using three-dimensional spherical polar Fourier (SPF) representations of protein shape. The approach is demonstrated by clustering subsets of the CATH database for each of the four main CATH fold types, and by searching the entire CATH database of some 12,000 structures using several protein structures as queries. Overall, the automatic SPF clustering approach agrees very well with the expert-curated CATH classification, and ROC plot analyses of the database searches show that the approach has very high precision and recall. Database query times can be reduced considerably by using a simple rotationally-invariant pre-filter in tandem with a more sensitive rotational search with little or no reduction in accuracy. Hence it should soon be possible to perform on-line 3D structural searches in interactive time-scales.
34 citations
TL;DR: An overview of applications of the deformable elastic network (DEN) refinement method is presented together with recommendations for its optimal usage.
Abstract: Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 A. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.
34 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Molecular replacement was performed with Phaser (McCoy et al., 2007) and yielded log-likelihood gain (LLG) and translation-function Z (TFZ) scores of 292 and 13, respectively....
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...The minimally optimized homology model as well as the template structure itself both yielded a molecular-replacement solution with Phaser (McCoy et al., 2007)....
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...The structure of MxA was determined by molecularreplacement phasing with Phaser (McCoy et al., 2007) using Acta Cryst....
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TL;DR: In this article, a molecular structure was established where a cyclohexenetrione moiety attached to O4 of a central glucose unit was in a hydrated six-membered hemiacetal ring structure, as expected from the NMR study of crystalline Geraniin.
Abstract: Geraniin, C41H28O27.7H2O, is the main tannin from Geranium thunbergii Sieb. et Zucc., which is one of the most popular folk medicines and also an official antidiarrheic drug in Japan. Conventional X-ray diffractometer data at 295 K and synchrotron data at 293 and 120 K (at EMBL/DESY Hamburg with a MARRESEARCH imaging plate) were measured. The structure could not be determined with any of the currently distributed direct-methods programs, but was easily solved with DIRDIF using several conformers of the hexahydroxydiphenoyl group as input fragments into a vector-search procedure. A molecular structure was established where a cyclohexenetrione moiety attached to O4 of a central glucose unit was in a hydrated six-membered hemiacetal ring structure, as expected from the NMR study of crystalline geraniin. Owing to the high oligocyclic substitution the glucopyranosyl ring is in the unusual 1C4 conformation. Refinement of the low-temperature synchrotron data allowed identification of almost all the H atoms, even within the seven water molecules, so that a rather complex system of approximately 30 different hydrogen bonds can be studied in some detail.
34 citations
References
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TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
34,239 citations
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.
28,425 citations
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.
27,505 citations
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
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.
18,531 citations
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.
17,755 citations