Match!

Diamonds in the rough: a strong case for the inclusion of weak‐intensity X‐ray diffraction data

Published on May 1, 2014in Acta Crystallographica Section D-biological Crystallography3.23
· DOI :10.1107/S1399004714005318
Jimin Wang44
Estimated H-index: 44
(Yale University),
Richard A. Wing4
Estimated H-index: 4
(Rockefeller University)
Cite
Abstract
Overwhelming evidence exists to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps improve the refinement of atomic models by imposing strong constraints on individual and overall temperature B factors and thus the quality of crystal structures. Some researchers consider these data to be of little value and opt to discard them during data processing, particularly at medium and low resolution, at which individual B factors of atomic models cannot be refined. Here, new evidence is provided to show that the inclusion of these data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry (NCS) averaging. Using electron-density correlation coefficients as criteria, the resolution of data has successfully been extended from 3.1 to 2.5 A resolution with redundancy-independent merging R factors from below 100% to about 310%. It is further demonstrated that phase information can be fully extracted from observed amplitudes through de novo NCS averaging. Averaging starts with uniform density inside double-shelled spherical masks and NCS matrices that are derived from bound heavy-atom clusters at the vertices of cuboctahedrally symmetric protein particles.
  • References (16)
  • Citations (9)
Cite
References16
Newest
Philip R. Evans41
Estimated H-index: 41
(LMB: Laboratory of Molecular Biology),
Garib N. Murshudov41
Estimated H-index: 41
(LMB: Laboratory of Molecular Biology)
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...
Published on May 6, 2013in Annual review of biophysics12.18
Paul D. Adams79
Estimated H-index: 79
(University of California, Berkeley),
David Baker129
Estimated H-index: 129
(UW: University of Washington)
+ 6 AuthorsThomas C. Terwilliger59
Estimated H-index: 59
(LANL: Los Alamos National Laboratory)
Advances in our understanding of macromolecular structure come from experimental methods, such as X-ray crystallography, and also computational analysis of the growing number of atomic models obtained from such experiments. The later analyses have made it possible to develop powerful tools for structure prediction and optimization in the absence of experimental data. In recent years, a synergy between these computational methods for crystallographic structure determination and structure predicti...
Published on Jan 18, 2013in Journal of Biological Chemistry
Richard D. Bunker12
Estimated H-index: 12
(University of Auckland),
Esther M. M. Bulloch11
Estimated H-index: 11
(University of Auckland)
+ 2 AuthorsEdward N. Baker63
Estimated H-index: 63
(University of Auckland)
d-Xylulokinase (XK; EC 2.7.1.17) catalyzes the ATP-dependent phosphorylation of d-xylulose (Xu) to produce xylulose 5-phosphate (Xu5P). In mammals, XK is the last enzyme in the glucuronate-xylulose pathway, active in the liver and kidneys, and is linked through its product Xu5P to the pentose-phosphate pathway. XK may play an important role in metabolic disease, given that Xu5P is a key regulator of glucose metabolism and lipogenesis. We have expressed the product of a putative human XK gene and...
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...
Jimin Wang44
Estimated H-index: 44
(Yale University)
It is common to report the resolution of a macromolecular structure with the highest resolution shell having an averaged I/σ(I) ≥ 2. Data beyond the resolution thus defined are weak and often poorly measured. The exclusion of these weak data may improve the apparent statistics and also leads to claims of lower resolutions that give some leniency in the acceptable quality of refined models. However, the inclusion of these data can provide additional strong constraints on atomic models during stru...
Paul Emsley20
Estimated H-index: 20
(University of Oxford),
Bernhard Lohkamp11
Estimated H-index: 11
(KI: Karolinska Institutet)
+ 1 AuthorsKevin Cowtan26
Estimated H-index: 26
(Ebor: University of York)
Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graph...
Published on Sep 1, 2009in Journal of Molecular Biology5.07
Frank DiMaio37
Estimated H-index: 37
(UW: University of Washington),
Michael D. Tyka15
Estimated H-index: 15
(UW: University of Washington)
+ 2 AuthorsDavid Baker129
Estimated H-index: 129
(UW: University of Washington)
Abstract We describe a method based on Rosetta structure refinement for generating high-resolution, all-atom protein models from electron cryomicroscopy density maps. A local measure of the fit of a model to the density is used to directly guide structure refinement and to identify regions incompatible with the density that are then targeted for extensive rebuilding. Over a range of test cases using both simulated and experimentally generated data, the method consistently increases the accuracy ...
Published on Apr 1, 2003in Journal of Molecular Biology5.07
Jimin Wang44
Estimated H-index: 44
(Yale University),
D.C. Boisvert1
Estimated H-index: 1
(Bayer USA: Bayer Corporation)
Abstract Nucleotide regulates the affinity of the bacterial chaperonin GroEL for protein substrates. GroEL binds protein substrates with high affinity in the absence of ATP and with low affinity in its presence. We report the crystal structure of (GroEL-KMgATP) 14 refined to 2.0 A resolution in which the ATP triphosphate moiety is directly coordinated by both K + and Mg 2+ . Upon the binding of KMgATP, we observe previously unnoticed domain rotations and a 102° rotation of the apical domain surf...
Gerard J. Kleywegt51
Estimated H-index: 51
(Uppsala University),
T.A. Jones32
Estimated H-index: 32
(Uppsala University)
Macromolecular phase-refinement and phase-extension calculations using real-space electron-density averaging techniques require accurate envelopes (or masks) to define the boundaries of each domain or molecule whose density is to be averaged. An extensive set of tools, implemented in four computer programs (O, MAMA, COMA and MASKIT) are described which can be used to generate such envelopes (either from an atomic model or based on local density-correlation maps), to improve them, to remove overl...
Published on Dec 1, 1998in Journal of Structural Biology3.75
Jimin Wang44
Estimated H-index: 44
(Yale University),
James A. Hartling2
Estimated H-index: 2
(BNL: Brookhaven National Laboratory),
John M. Flanagan27
Estimated H-index: 27
(BNL: Brookhaven National Laboratory)
Abstract Large ATP-dependent proteolytic complexes carry out the majority of intracellular proteolysis. To begin to understand the function of these proteases at a structural level, we have combined the information from a number of biophysical techniques such as electron microscopy (EM), small-angle scattering, and x-ray crystallography. In this study, we exploited the inherent symmetry of Escherichia coli ClpP, the proteolytic component of the ClpAP/XP ATP-dependent protease, to determine its x...
Cited By9
Newest
Published on Dec 1, 2019
Hsin-Hui Wu (RFUMS: Rosalind Franklin University of Medicine and Science), Jindrich Symersky5
Estimated H-index: 5
(RFUMS: Rosalind Franklin University of Medicine and Science),
Min Lu8
Estimated H-index: 8
(RFUMS: Rosalind Franklin University of Medicine and Science)
MdfA is a prototypical H+-coupled multidrug transporter that is characterized by extraordinarily broad substrate specificity. The involvement of specific H-bonds in MdfA-drug interactions and the simplicity of altering the substrate specificity of MdfA contradict the promiscuous nature of multidrug recognition, presenting a baffling conundrum. Here we show the X-ray structures of MdfA variant I239T/G354E in complexes with three electrically different ligands, determined at resolutions up to 2.2 ...
Published on Aug 22, 2019in Molecules3.06
Saara Laulumaa5
Estimated H-index: 5
,
Petri Kursula27
Estimated H-index: 27
Myelin protein 2 (P2) is a peripheral membrane protein of the vertebrate nervous system myelin sheath, having possible roles in both lipid transport and 3D molecular organization of the multilayered myelin membrane. We extended our earlier crystallographic studies on human P2 and refined its crystal structure at an ultrahigh resolution of 0.72 A in perdeuterated form and 0.86 A in hydrogenated form. Characteristic differences in C–H…O hydrogen bond patterns were observed between extended β stran...
Published on Feb 1, 2018in Protein Science2.42
Jimin Wang44
Estimated H-index: 44
(Yale University)
Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large macromolecular complexes with a reduced occupancy or an increased atomic mobility or both due to affinity-based functional regulation, and so may substrates, products, cofactors, ions or solvent molecule to the active sites of enzymes. A quantitative...
Published on Dec 1, 2017in Protein Science2.42
Jimin Wang44
Estimated H-index: 44
(Yale University),
Gary W. Brudvig71
Estimated H-index: 71
(Yale University)
+ 1 AuthorsPeter B. Moore46
Estimated H-index: 46
(Yale University)
In 2012, Karplus and Diederichs demonstrated that the Pearson correlation coefficient CC1/2 is a far better indicator of the quality and resolution of crystallographic data sets than more traditional measures like merging R-factor or signal-to-noise ratio. More specifically, they proposed that CC1/2 be computed for data sets in thin shells of increasing resolution so that the resolution dependence of that quantity can be examined. Recently, however, the CC1/2 values of entire data sets, i.e. cum...
Published on Oct 13, 2017in ACS energy letters16.33
Jimin Wang44
Estimated H-index: 44
(Yale University),
Mikhail Askerka9
Estimated H-index: 9
(Yale University)
+ 1 AuthorsVictor S. Batista46
Estimated H-index: 46
(Yale University)
Photosystem II (PSII) oxidizes water to produce oxygen through a four-step photocatalytic cycle. Understanding PSII structure–function relations is important for the development of biomimetic photocatalytic systems. The quantum mechanics/molecular mechanics (QM/MM) analysis of substrate water binding to the oxygen-evolving complex (OEC) has suggested a rearrangement of water ligands in a carousel mechanism around a key Mn center. Here, we find that the most recently reported X-ray free-electron ...
Published on Feb 10, 2017in ACS energy letters16.33
Jimin Wang44
Estimated H-index: 44
(Yale University),
Mikhail Askerka9
Estimated H-index: 9
(Yale University)
+ 1 AuthorsVictor S. Batista46
Estimated H-index: 46
(Yale University)
Understanding structure–function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main ...
Published on Nov 1, 2015in Nature Communications11.88
D.A. WinkelmannD20
Estimated H-index: 20
,
Eva Forgacs11
Estimated H-index: 11
+ 1 AuthorsAnn M. Stock49
Estimated H-index: 49
Omecamtiv Mecarbil (OM) is a small molecule allosteric effector of cardiac myosin that is in clinical trials for treatment of systolic heart failure. A detailed kinetic analysis of cardiac myosin has shown that the drug accelerates phosphate release by shifting the equilibrium of the hydrolysis step towards products, leading to a faster transition from weak to strong actin-bound states. The structure of the human β-cardiac motor domain (cMD) with OM bound reveals a single OM-binding site nestled...
Published on Oct 1, 2015in Current Opinion in Structural Biology7.05
P. Andrew Karplus46
Estimated H-index: 46
(OSU: Oregon State University),
Kay Diederichs51
Estimated H-index: 51
(University of Konstanz)
The quality of macromolecular crystal structures depends, in part, on the quality and quantity of the data used to produce them. Here, we review recent shifts in our understanding of how to use data quality indicators to select a high resolution cutoff that leads to the best model, and of the potential to greatly increase data quality through the merging of multiple measurements from multiple passes of single crystals or from multiple crystals. Key factors supporting this shift are the introduct...
Published on May 1, 2015in Protein Science2.42
Jimin Wang44
Estimated H-index: 44
(Yale University)
In 2008, Zwart and colleagues observed that the fraction of the structures deposited in the PDB alleged to have “pseudosymmetry” or “special noncrystallographic symmetry” (NCS) was about 6%, and that this percentage was rising annually. A few years later, Poon and colleagues found that 2% of all the crystal structures in the PDB belonged to higher symmetry space groups than those assigned to them. Here, I report an analysis of the X-ray diffraction data deposited for this class of structures, wh...
Published on May 1, 2015in Protein Science2.42
Jimin Wang44
Estimated H-index: 44
(Yale University)
Crystallographic Rwork and Rfree values, which are measures of the ability of the models of macromolecular structures to explain the crystallographic data on which they are based, are often used to assess structure quality. It is widely known, and confirmed here that both are sensitive to the methods used to compute them, and can be manipulated to improve the apparent quality of the model. As an alternative it is proposed here that the quality of crystallographic models should be assessed using ...
View next paper[19]Study of protein dynamics by X-ray diffraction