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How good are my data and what is the resolution

Published on Jul 1, 2013in Acta Crystallographica Section D-biological Crystallography3.23
· DOI :10.1107/S0907444913000061
Philip R. Evans41
Estimated H-index: 41
(LMB: Laboratory of Molecular Biology),
Garib N. Murshudov41
Estimated H-index: 41
(LMB: Laboratory of Molecular Biology)
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Abstract
Following integration of the observed diffraction spots, the process of `data reduction' initially aims to determine the point-group symmetry of the data and the likely space group. This can be performed with the program POINTLESS. The scaling program then puts all the measurements on a common scale, averages measurements of symmetry-related reflections (using the symmetry determined previously) and produces many statistics that provide the first important measures of data quality. A new scaling program, AIMLESS, implements scaling models similar to those in SCALA but adds some additional analyses. From the analyses, a number of decisions can be made about the quality of the data and whether some measurements should be discarded. The effective `resolution' of a data set is a difficult and possibly contentious question (particularly with referees of papers) and this is discussed in the light of tests comparing the data-processing statistics with trials of refinement against observed and simulated data, and automated model-building and comparison of maps calculated with different resolution limits. These trials show that adding weak high-resolution data beyond the commonly used limits may make some improvement and does no harm.
  • References (22)
  • Citations (1203)
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References22
Newest
Qun Liu29
Estimated H-index: 29
(BNL: Brookhaven National Laboratory),
Wayne A. Hendrickson83
Estimated H-index: 83
Structure determinations for biological macromolecules that have no known structural antecedents typically involve the incorporation of heavier atoms than those found natively in biological molecules. Currently, selenomethionyl proteins analyzed using single- or multi-wavelength anomalous diffraction (SAD or MAD) data predominate for such de novo analyses. Naturally occurring metal ions such as zinc or iron often suffice in MAD or SAD experiments, and sulfur SAD has been an option since it was f...
Rita Giordano2
Estimated H-index: 2
,
Ricardo M. F. Leal6
Estimated H-index: 6
+ 2 AuthorsAlexander Popov11
Estimated H-index: 11
It is generally assumed that the quality of X-ray diffraction data can be improved by merging data sets from several crystals. However, this effect is only valid if the data sets used are from crystals that are structurally identical. It is found that frozen macromolecular crystals very often have relatively low structure identity (and are therefore not isomorphous); thus, to obtain a real gain from multi-crystal data sets one needs to make an appropriate selection of structurally similar crysta...
Published on May 25, 2012in Science41.04
Qun Liu29
Estimated H-index: 29
(BNL: Brookhaven National Laboratory),
Tassadite Dahmane3
Estimated H-index: 3
(Columbia University)
+ 5 AuthorsWayne A. Hendrickson83
Estimated H-index: 83
Crystal structure analyses for biological macromolecules without known structural relatives entail solving the crystallographic phase problem. Typical de novo phase evaluations depend on incorporating heavier atoms than those found natively; most commonly, multi- or single-wavelength anomalous diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here, we realize routine structure determination using intrinsic anomalous scattering from native macromolecules. We devised robust pr...
Published on May 25, 2012in Science41.04
P. Andrew Karplus46
Estimated H-index: 46
(OSU: Oregon State University),
Kay Diederichs51
Estimated H-index: 51
(University of Konstanz)
In macromolecular x-ray crystallography, refinement R values measure the agreement between observed and calculated data. Analogously, R merge values reporting on the agreement between multiple measurements of a given reflection are used to assess data quality. Here, we show that despite their widespread use, R merge values are poorly suited for determining the high-resolution limit and that current standard protocols discard much useful data. We introduce a statistic that estimates the correlati...
Kevin Cowtan26
Estimated H-index: 26
(Ebor: University of York)
Two developments in the process of automated protein model building in the Buccaneer software are presented. A general-purpose library for protein fragments of arbitrary size is described, with a highly optimized search method allowing the use of a larger database than in previous work. The problem of assembling an autobuilt model into complete chains is discussed. This involves the assembly of disconnected chain fragments into complete molecules and the use of the database of protein fragments ...
Published on Feb 1, 2012in Structure4.58
Richard Henderson60
Estimated H-index: 60
(LMB: Laboratory of Molecular Biology),
Andrej Sali95
Estimated H-index: 95
(UCSF: University of California, San Francisco)
+ 25 AuthorsNikolaus Grigorieff54
Estimated H-index: 54
(HHMI: Howard Hughes Medical Institute)
This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models...
Philip R. Evans41
Estimated H-index: 41
(LMB: Laboratory of Molecular Biology)
This paper presents an overview of how to run the CCP4 programs for data reduction (SCALA, POINTLESS and CTRUNCATE) through the CCP4 graphical interface ccp4i and points out some issues that need to be considered, together with a few examples. It covers determination of the point-group symmetry of the diffraction data (the Laue group), which is required for the subsequent scaling step, examination of systematic absences, which in many cases will allow inference of the space group, putting multip...
Winn7
Estimated H-index: 7
(Daresbury Laboratory),
Charles Ballard3
Estimated H-index: 3
(RAL: Rutherford Appleton Laboratory)
+ 15 AuthorsAirlie J. McCoy34
Estimated H-index: 34
(University of Cambridge)
The CCP4 (Collaborative Computational Project, Number 4) software suite is a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims. The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. Struc...
Garib N. Murshudov41
Estimated H-index: 41
(Ebor: University of York),
Pavol Skubák8
Estimated H-index: 8
(LEI: Leiden University)
+ 6 AuthorsA.A. Vagin8
Estimated H-index: 8
(Ebor: University of York)
This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model par...
Kay Diederichs51
Estimated H-index: 51
(University of Konstanz)
An indicator which is calculated after the data reduction of a test data set may be used to estimate the (systematic) instrument error at a macromolecular X-ray source. The numerical value of the indicator is the highest signal-to-noise [I/� (I)] value that the experimental setup can produce and its reciprocal is related to the lower limit of the merging R factor. In the context of this study, the stability of the experimental setup is influenced and characterized by the properties of the X-ray ...
Cited By1203
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Published on Dec 1, 2019in Nature Communications11.88
Aurelia Stangl , Paul R. Elliott (University of Oxford)+ 10 AuthorsFarid El Oualid14
Estimated H-index: 14
OTULIN (OTU Deubiquitinase With Linear Linkage Specificity) specifically hydrolyzes methionine1 (Met1)-linked ubiquitin chains conjugated by LUBAC (linear ubiquitin chain assembly complex). Here we report on the mass spectrometric identification of the OTULIN interactor SNX27 (sorting nexin 27), an adaptor of the endosomal retromer complex responsible for protein recycling to the cell surface. The C-terminal PDZ-binding motif (PDZbm) in OTULIN associates with the cargo-binding site in the PDZ do...
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Tomáš Kovaľ3
Estimated H-index: 3
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Leona Švecová1
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(CTU: Czech Technical University in Prague)
+ 8 AuthorsMária Trundová2
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Published on Mar 6, 2019in Scientific Reports4.01
Estefania O. Juárez-Hernández2
Estimated H-index: 2
(Universidad de Guanajuato),
Luz E. Casados-Vázquez5
Estimated H-index: 5
(Universidad de Guanajuato)
+ 3 AuthorsJosé E. Barboza-Corona10
Estimated H-index: 10
(Universidad de Guanajuato)
There is no structural information about any chitinase synthesized by Bacillus thuringiensis, the most successful microbial insect larvicide used worldwide. In this study, we solved the 3D structure of the chitinase ChiA74 at 2.26 A. The crystal structure shows that ChiA74 is composed of a modular arrangement formed by (i) a catalytic region (CD), (ii) a chitinase insertion domain (CID), (iii) a fibronectin type III domain (FnIII), and (iv) a chitin binding domain (CBD). The location of the CBD ...
Published on Dec 1, 2019in Nature Communications11.88
Rafael Molina13
Estimated H-index: 13
(UCPH: University of Copenhagen),
Stefano Stella10
Estimated H-index: 10
(UCPH: University of Copenhagen)
+ 6 AuthorsGuillermo Montoya30
Estimated H-index: 30
(UCPH: University of Copenhagen)
Type III CRISPR-Cas multisubunit complexes cleave ssRNA and ssDNA. These activities promote the generation of cyclic oligoadenylate (cOA), which activates associated CRISPR-Cas RNases from the Csm/Csx families, triggering a massive RNA decay to provide immunity from genetic invaders. Here we present the structure of Sulfolobus islandicus (Sis) Csx1-cOA4 complex revealing the allosteric activation of its RNase activity. SisCsx1 is a hexamer built by a trimer of dimers. Each dimer forms a cOA4 bin...
Published on Dec 1, 2019in Nature Communications11.88
Ian R. Monk20
Estimated H-index: 20
(University of Melbourne),
Nausad Shaikh1
Estimated H-index: 1
(UQ: University of Queensland)
+ 18 AuthorsBrit Winnen6
Estimated H-index: 6
WalKR (YycFG) is the only essential two-component regulator in the human pathogen Staphylococcus aureus. WalKR regulates peptidoglycan synthesis, but this function alone does not explain its essentiality. Here, to further understand WalKR function, we investigate a suppressor mutant that arose when WalKR activity was impaired; a histidine to tyrosine substitution (H271Y) in the cytoplasmic Per-Arnt-Sim (PASCYT) domain of the histidine kinase WalK. Introducing the WalKH271Y mutation into wild-typ...
Published on Jan 1, 2019in Nature Communications11.88
E. Errasti3
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E. Errasti-Mururgarren + 9 AuthorsMeritxell Espino-Guarch (Qatar Airways)
L-amino acid transporters (LATs) play key roles in human physiology and are implicated in several human pathologies. LATs are asymmetric amino acid exchangers where the low apparent affinity cytoplasmic side controls the exchange of substrates with high apparent affinity on the extracellular side. Here, we report the crystal structures of an LAT, the bacterial alanine-serine-cysteine exchanger (BasC), in a non-occluded inward-facing conformation in both apo and substrate-bound states. We crystal...
Published on Dec 1, 2019in Nature Communications11.88
Bo Zhang (Fujian Normal University), Yangmiao Ye (Fujian Normal University)+ 10 AuthorsSiqi Wang (Fujian Normal University)
Cas13d, the type VI-D CRISPR-Cas effector, is an RNA-guided ribonuclease that has been repurposed to edit RNA in a programmable manner. Here we report the detailed structural and functional analysis of the uncultured Ruminococcus sp. Cas13d (UrCas13d)-crRNA complex. Two hydrated Mg2+ ions aid in stabilizing the conformation of the crRNA repeat region. Sequestration of divalent metal ions does not alter pre-crRNA processing, but abolishes target cleavage by UrCas13d. Notably, the pre-crRNA proces...
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(UCL: University College London),
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(UCL: University College London)
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Desensitization is a canonical property of ligand-gated ion channels, causing progressive current decline in the continued presence of agonist. AMPA-type glutamate receptors (AMPARs), which mediate fast excitatory signaling throughout the brain, exhibit profound desensitization. Recent cryo-EM studies of AMPAR assemblies show their ion channels to be closed in the desensitized state. Here we present evidence that homomeric Q/R-edited AMPARs still allow ions to flow when the receptors are desensi...
Published on Apr 4, 2019in Nature Communications11.88
Mintu Chandra3
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(UQ: University of Queensland),
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Phox homology (PX) domains are membrane interacting domains that bind to phosphatidylinositol phospholipids or phosphoinositides, markers of organelle identity in the endocytic system. Although many PX domains bind the canonical endosome-enriched lipid PtdIns3P, others interact with alternative phosphoinositides, and a precise understanding of how these specificities arise has remained elusive. Here we systematically screen all human PX domains for their phospholipid preferences using liposome b...
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Estimated H-index: 7
(UR: University of Rochester)
Mutations of human BEST1, encoding a Ca2+-activated Cl− channel (hBest1), cause macular degenerative disorders. Best1 homolog structures reveal an evolutionarily conserved channel architecture highlighted by two landmark restrictions (named the “neck” and “aperture”, respectively) in the ion conducting pathway, suggesting a unique dual-switch gating mechanism, which, however, has not been characterized well. Using patch clamp and crystallography, we demonstrate that both the neck and aperture in...
View next paperThe CCP4 suite: programs for protein crystallography.