scholarly journals Measuring and modeling diffuse scattering in protein X-ray crystallography

2015 ◽  
Author(s):  
Andrew H. Van Benschoten ◽  
Lin Liu ◽  
Ana Gonzalez ◽  
Aaron S. Brewster ◽  
Nicholas K. Sauter ◽  
...  
Keyword(s):  
Data Collection ◽  
Diffuse Scattering ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Coarse Grained ◽  
X Ray Diffraction ◽  
Diffuse Intensity ◽  
X Ray ◽  
Protein Motions ◽  
Extra Effort

AbstractX-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations must be measured. Until now measurement of diffuse scattering from protein crystals has been scarce, due to the extra effort of collecting diffuse data. Here, we present three-dimensional measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested Translation-Libration-Screw (TLS), Liquid-Like Motions (LLM), and coarse-grained Normal Modes (NM) models of protein motions. The LLM model provides a global picture of motions and were refined against the diffuse data, while the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that NM-based refinement can generate dynamics-inspired structural models that simultaneously agree with both Bragg and diffuse scattering.SignificanceThe structural details of protein motions are critical to understanding many biological processes, but they are often hidden to conventional biophysical techniques. Diffuse X-ray scattering can reveal details of the correlated movements between atoms; however, the data collection historically has required extra effort and dedicated experimental protocols. We have measured three-dimensional diffuse intensities in X-ray diffraction from CypA and trypsin crystals using standard crystallographic data collection techniques. Analysis of the resulting data is consistent with the protein motions resembling diffusion in a liquid or vibrations of a soft solid. Our results show that using diffuse scattering to model protein motions can become a component of routine crystallographic analysis through the extension of commonplace methods.

scholarly journals Measuring and modeling diffuse scattering in protein X-ray crystallography

2016 ◽  
Vol 113 (15) ◽  
pp. 4069-4074 ◽  
Author(s):  
Andrew H. Van Benschoten ◽  
Lin Liu ◽  
Ana Gonzalez ◽  
Aaron S. Brewster ◽  
Nicholas K. Sauter ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Structure Refinement ◽  
Normal Modes ◽  
Coarse Grained ◽  
X Ray Diffraction ◽  
Diffuse Intensity ◽  
X Ray ◽  
Protein Motions ◽  
X Ray Crystallography ◽  
Standard Data

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.

Structure Refinement of CePtSi and Hydrogenation Behavior of CePdGe, CePtSi and CePtGe

2007 ◽  
Vol 62 (4) ◽  
pp. 613-616 ◽  
Author(s):  
Wilfried Hermes ◽  
Ute Ch. Rodewald ◽  
Bernard Chevalier ◽  
Rainer Pötgena
Keyword(s):  
Single Crystal ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Subsequent Annealing ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydride Formation ◽  
Arc Melting ◽  
Cerium Compounds

The intermetallic cerium compounds CePdGe, CePtSi, and CePtGe were synthesized from the elements by arc-melting and subsequent annealing. The structure of CePtSi was refined from single crystal X-ray diffraction data: LaPtSi-type (ordered α-ThSi2 version), 141md, a = 419.6(1) and c = 1450.0(5) pm, wR2 = 0.0490, 362 F2 values and 16 variables. The Pt-Si distances within the three-dimensional [PtSi] network are 242 pm, indicating strong Pt-Si interactions. Hydrogenation of the three compounds at 623 K and 4 MPa H2 gave no indication for hydride formation.

In Situ Three-Dimensional Orientation Mapping in Plastically-Deformed Polycrystalline Iron by Three-Dimensional X-Ray Diffraction

2014 ◽  
Vol 777 ◽  
pp. 118-123 ◽  
Author(s):  
Yujiro Hayashi ◽  
Yoshiharu Hirose ◽  
Daigo Setoyama
Keyword(s):  
Three Dimensional ◽  
Diffraction Method ◽  
Inverse Pole Figure ◽  
Coarse Grained ◽  
Uniaxial Tensile ◽  
X Ray Diffraction ◽  
Polycrystalline Iron ◽  
X Ray ◽  
Orientation Mapping

In situ three-dimensional crystallographic orientation mapping in plastically-deformed polycrystalline iron is demonstrated using a modified three-dimensional x-ray diffraction method. This voxel-by-voxel measurement method enables the observation of intragranular orientation distribution. The experiment is performed using coarse-grained ferrite with a mean grain size of ~ 60 μm and an incident x-ray beam with a beam size of 20 μm × 20 μm. Grains averagely rotate approximately toward the <110> preferred orientation of body-centered cubic uniaxial tensile texture. Intragranular orientation distributions are spread as the tensile strain increases to 10.7 %. Furthermore, intragranular multidirectional rotations are observed in grains near the <100> and <111> corners in the inverse pole figure.

Diffuse scattering in protein crystallography

1995 ◽  
Vol 28 (2) ◽  
pp. 131-169 ◽  
Author(s):  
Jean-Pierre Benoit ◽  
Jean Doucet
Keyword(s):  
Molecular Biology ◽  
Active Site ◽  
Diffuse Scattering ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Physico Chemical ◽  
Chemical Conditions ◽  
Functional Mechanisms

The understanding of flexibility and deformability in proteins is one of the current major challenges of structural molecular biology. The knowledge of the average atomic positions of three-dimensional folding of proteins, which is obtained either by X-ray diffraction or n.m.r. spectroscopy, is generally not sufficient to explain their functional mechanisms. Very often it is necessary to consider the existence of other concerted atomic motions as, for example, in the well-known case of the CO molecule fixation at the active site of myoglobin which requires the concerted displacement of a large number of atoms in order to open a channel down to this site. This opening, which depends on the physico-chemical conditions, plays the role of a regulator in the biochemical reactions (Janin & Wodak, 1983; Tainer et al. 1984; Westhof et al. 1984; Ormos et al. 1988).

scholarly journals Current approaches for the fitting and refinement of atomic models into cryo-EM maps usingCCP-EM

2018 ◽  
Vol 74 (6) ◽  
pp. 492-505 ◽  
Author(s):  
Robert A. Nicholls ◽  
Michal Tykac ◽  
Oleg Kovalevskiy ◽  
Garib N. Murshudov
Keyword(s):  
Fourier Coefficients ◽  
Structure Refinement ◽  
Point Group ◽  
Three Dimensional ◽  
Divide And Conquer ◽  
X Ray Diffraction ◽  
Molecular Visualization ◽  
Macromolecular Complexes ◽  
X Ray ◽  
Atomic Models

Recent advances in instrumentation and software have resulted in cryo-EM rapidly becoming the method of choice for structural biologists, especially for those studying the three-dimensional structures of very large macromolecular complexes. In this contribution, the tools available for macromolecular structure refinement into cryo-EM reconstructions that are availablevia CCP-EMare reviewed, specifically focusing onREFMAC5 and related tools. Whilst originally designed with a view to refinement against X-ray diffraction data, some of these tools have been able to be repurposed for cryo-EM owing to the same principles being applicable to refinement against cryo-EM maps. Since both techniques are used to elucidate macromolecular structures, tools encapsulating prior knowledge about macromolecules can easily be transferred. However, there are some significant qualitative differences that must be acknowledged and accounted for; relevant differences between these techniques are highlighted. The importance of phases is considered and the potential utility of replacing inaccurate amplitudes with their expectations is justified. More pragmatically, an upper bound on the correlation between observed and calculated Fourier coefficients, expressed in terms of the Fourier shell correlation between half-maps, is demonstrated. The importance of selecting appropriate levels of map blurring/sharpening is emphasized, which may be facilitated by considering the behaviour of the average map amplitude at different resolutions, as well as the utility of simultaneously viewing multiple blurred/sharpened maps. Features that are important for the purposes of computational efficiency are discussed, notably theDivide and Conquerpipeline for the parallel refinement of large macromolecular complexes. Techniques that have recently been developed or improved inCootto facilitate and expedite the building, fitting and refinement of atomic models into cryo-EM maps are summarized. Finally, a tool for symmetry identification from a given map or coordinate set,ProSHADE, which can identify the point group of a map and thus may be used during deposition as well as during molecular visualization, is introduced.

Structure refinement of the layered composite crystal Sc2B1.1C3.2 in a five-dimensional formalism

2001 ◽  
Vol 57 (4) ◽  
pp. 449-457 ◽  
Author(s):  
Mitsuko Onoda ◽  
Ying Shi ◽  
A. Leithe-Jasper ◽  
Takaho Tanaka
Keyword(s):  
Structural Parameters ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Layered Composite ◽  
Layered Compound ◽  
X Ray Diffraction ◽  
X Ray ◽  
Composite Crystal ◽  
The Difference ◽  
Insight Into

The crystal structure of a layered compound Sc2B1.1C3.2, scandium boride carbide (M r = 140.43), has been re-refined as a commensurate composite crystal using 1795 single-crystal X-ray diffraction intensities with I > 2\sigma(I) collected by Shi, Leithe-Jasper, Bourgeois, Bando & Tanaka [(1999), J. Solid State Chem. 148, 442–449]. The crystal is composed of two layered subsystem structures, i.e. Sc—C—Sc sandwiches and graphite-like layers of the composition B1/3C2/3. The structure refinement was performed in a five-dimensional formalism based on the trigonal superspace group P\bar{3}m1(p00)(0p0)0m0. The unit cell and other crystal data are a = b = 3.387 (1), c = 6.703 (2) Å, V = 66.59 (1) Å3, \boldsigma_{1} = (9/7 0 0), \boldsigma_{2} = (0 9/7 0), Z = 1, D x = 3.501 Mg m−1. Two different three-dimensional sections through the superspace were analyzed, corresponding to two different superstructure models, one with P\bar{3}m1 and the other with P\bar{3}m1. A random distribution of B and C was assumed in the graphite-like layer and 41 structural parameters were introduced. R F /wR F } were 0.0533/0.0482 and 0.0524/0.0476, respectively, for the first and second models. Although the difference between these R F or wR F values was too fine to exclude one of the models definitely, the advantages of using a superspace group were obvious. It not only brought about better convergence of refinement cycles by virtue of fewer parameters, but also gave an insight into the problem of symmetry of the superstructure.

scholarly journals Quantitative grain-scale ferroic domain volume fractions and domain switching strains from three-dimensional X-ray diffraction data

2015 ◽  
Vol 48 (3) ◽  
pp. 882-889 ◽  
Author(s):  
Jette Oddershede ◽  
Marta Majkut ◽  
Qinghua Cao ◽  
Søren Schmidt ◽  
Jonathan P. Wright ◽  
...  
Keyword(s):  
Domain Switching ◽  
Volume Fraction ◽  
Three Dimensional ◽  
Bulk Sample ◽  
Coarse Grained ◽  
X Ray Diffraction ◽  
X Ray ◽  
Volume Fractions ◽  
Fine Grained ◽  
Ferroic Materials

A method for the extension of the three-dimensional X-ray diffraction technique to allow the extraction of domain volume fractions in polycrystalline ferroic materials is presented. This method gives access to quantitative domain volume fractions of hundreds of independent embedded grains within a bulk sample. Such information is critical to furthering our understanding of the grain-scale interactions of ferroic domains and their influence on bulk properties. The method also provides a validation tool for mesoscopic ferroic domain modelling efforts. The mathematical formulations presented here are applied to tetragonal coarse-grained Ba0.88Ca0.12Zr0.06Ti0.94O3and rhombohedral fine-grained (0.82)Bi0.5Na0.5TiO3–(0.18)Bi0.5K0.5TiO3electroceramic materials. The fitted volume fraction information is used to calculate grain-scale non-180° ferroelectric domain switching strains. The absolute errors are found to be approximately 0.01 and 0.03% for the tetragonal and rhombohedral cases, which had maximum theoretical domain switching strains of 0.47 and 0.54%, respectively. Limitations and possible extensions of the technique are discussed.

Structure Refinement and Magnetic Properties of Ce2RuAl3 and a Group-Subgroup Scheme for Ce5Ru3Al2

2011 ◽  
Vol 66 (8) ◽  
pp. 771-776 ◽  
Author(s):  
Trinath Mishra ◽  
Rolf-Dieter Hoffmann ◽  
Christian Schwickert ◽  
Rainer Pöttgen
Keyword(s):  
Magnetic Properties ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Structural Distortions ◽  
Dimensional Network ◽  
Subgroup Scheme

The hexagonal Laves phase Ce2RuAl3 (≡ CeRu0.5Al1.5) was synthesized by high-frequencemelting of the elements in a sealed tantalum tube and subsequent annealing. The structure was refined from single-crystal X-ray diffraction data: MgZn2 type, P63/mmc, Z = 2, a = 565.38(9), c = 888.3(1) pm, wR2 = 0.0231, 193 F2 values and 13 parameters. The 2a (0.824 Ru + 0.176 Al) and 6h (0.956 Al + 0.044 Ru) Wyckoff positions show mixed occupancies leading to the composition CeRu0.48Al1.52 for the investigated crystal. The aluminum atoms build up Kagomé networks at z = 1/4 and z = 3/4 which are connected to a three-dimensional network by the ruthenium atoms. The cerium atoms fill cavities of coordination number 16 (3 Ru + 9 Al + 4 Ce) within the [RuAl3] network. The Ce2RuAl3 sample orders ferromagnetically at TC = 8.0(1) K. The cerium-rich aluminide Ce5Ru3Al2 shows unusually short Ce-Ru distances of 253 and 260 pm for the Ce1 position as a result of intermediate cerium valence. The structural distortions are discussed on the basis of a group-subgroup scheme for Pr5Ru3Al2 (space group I213) and the superstructure variant Ce5Ru3Al2 (space group R3).

scholarly journals Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders

IUCrJ ◽  
2015 ◽  
Vol 2 (2) ◽  
pp. 267-282 ◽  
Author(s):  
Yifeng Yun ◽  
Xiaodong Zou ◽  
Sven Hovmöller ◽  
Wei Wan
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Structure Determination ◽  
Three Dimensional ◽  
Structure Identification ◽  
Phase Identification ◽  
Dimensional Electron ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution

Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni–Se–O–Cl crystals, zeolites, germanates, metal–organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods will become crucially important in the near future.

Neutronen- und Röntgenbeugungsuntersuchungen an Pulvern und Einkristallen von Strukturverwandten des Berliner Blaus: CsMnIICrIII(CN)6 · D2O , NMe4MnII(Cr0,06,Mn0,94)III(CN)6 · 8 H2O , NMe4MnIICoIII(CN)6 · 8 H20 , Mn3II[MnIII(CN)6]2 · 15 H2O und Cd3[FeIII(CN)6]2 · 15 H2O / Neutron and X-Ray Diffraction Studies on Powders and Single Crystals of Compounds Structurally Related to Prussian Blue: CsMnIICrIII(CN)6 · D2O, NMe4MnII(Cr0,06Mn0,94)III(CN)6 · 8 H2O, NMe4MnIICoIII(CN)6 · 8 H2O, Mn3II[MnIII(CN)6]2 · 15 H2O and Cd3[FeIII(CN)6]2 · 15 H2O

1999 ◽  
Vol 54 (7) ◽  
pp. 870-876 ◽  
Author(s):  
Bernd Ziegler ◽  
Michael Witzel ◽  
Martin Schwarten ◽  
Dietrich Babel
Keyword(s):  
Crystal Structure ◽  
Ambient Temperature ◽  
Single Crystal ◽  
Single Crystals ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Crystal Structure Refinement ◽  
X Ray Diffraction ◽  
One Dimensional ◽  
X Ray

The results of a Rietveld refinement of CsMnCr(CN)6 · D2O neutron powder data (a = 1084.3(1) pm, F4̄3m, Z = 4) and of a neutron single crystal structure refinement of tetragonal NMe4MnII(Cr0,06Mn0,94)III(CN)6 · 8 H2O (a = 1065.8(21), c = 1064.6(26) pm, P4/n, Z = 2) at ambient temperature are reported. Single crystal X-ray analyses of the isostructural octahydrate NMe4MnCo(CN)6 · 8 H20 (a = 1062.1 (1), c = 1046.2( 1) pm) and of gel-grown crystals of cubic Mn3II[MnIII(CN)6]2 - 15 H2O (a = 1062.6(3) pm, Fm3̄m, Z = 4/3) and Cd3[Fe(CN)6]2 · 15 H2O (a = 1067.7(3) pm) were performed as well. The latter “Prussian Blues” are highly disordered and intermediate with respect to cyano-bridging between the above three-dimensional cesium and one-dimensional tetramethylammonium compounds.

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