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 Linear Structural Trends and Multi-Phase Intergrowths in Helvine-Group Minerals, (Zn,Fe,Mn)8[Be6Si6O24]S2

Minerals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 325
Author(s):  
Sytle Antao
Keyword(s):  
Cell Parameter ◽  
Structural Parameters ◽  
Unit Cell ◽  
Fluid Composition ◽  
Ternary Solid Solution ◽  
X Ray Diffraction ◽  
X Ray ◽  
The Difference ◽  
Multi Phase ◽  
And Diffusion

Synchrotron high-resolution powder X-ray diffraction (HRPXRD) and Rietveld structure refinements were used to examine the crystal structure of single phases and intergrowths (either two or three phases) in 13 samples of the helvine-group minerals, (Zn,Fe,Mn)8[Be6Si6O24]S2. The helvine structure was refined in the cubic space group P4¯3n. For the intergrowths, simultaneous refinements were carried out for each phase. The structural parameters for each phase in an intergrowth are only slightly different from each other. Each phase in an intergrowth has well-defined unit-cell and structural parameters that are significantly different from the three endmembers and these do not represent exsolution or immiscibility gaps in the ternary solid-solution series. The reason for the intergrowths in the helvine-group minerals is not clear considering the similar radii, identical charge, and diffusion among the interstitial M cations (Zn2+, Fe2+, and Mn2+) that are characteristic of elongated tetrahedral coordination. The difference between the radii of Zn2+ and Mn2+ cations is 10%. Depending on the availability of the M cations, intergrowths may occur as the temperature, pressure, fugacity fS2, and fluid composition change on crystallization. The Be–Si atoms are fully ordered. The Be–O and Si–O distances are nearly constant. Several structural parameters (Be–O–Si bridging angle, M–O, M–S, average <M–O/S>[4] distances, and TO4 rotational angles) vary linearly with the a unit-cell parameter across the series because of the size of the M cation.

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.

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.

Atomic displacement parameters for Ni(ND3)4(NO2)2 from 9 K X-ray and 13 K time-of-flight neutron diffraction data

1996 ◽  
Vol 52 (6) ◽  
pp. 923-931 ◽  
Author(s):  
B. B. Iversen ◽  
F. K. Larsen ◽  
B. N. Figgis ◽  
P. A. Reynolds ◽  
A. J. Schultz
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Structural Information ◽  
Structural Parameters ◽  
Structure Refinement ◽  
Time Of Flight ◽  
Thermal Parameters ◽  
Neutron Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray

Structural parameters derived from 9 1) K X-ray diffraction data and 13 (1) K time-of-flight neutron diffraction data on perdeuterated tetraamminedinitronickel(II), Ni(ND3)4(NO2)2, are compared. It is shown that excellent agreement can be obtained for both positional and thermal parameters derived separately from the two experiments, provided that great care is taken in all steps of the process, including data collection, data reduction, and nuclear and electronic structure refinement. The mean difference in the thermal parameters, <|ΔUij |>, is as low as 0.00034 Å2 and <(ΔUij/σ)2>1/2 = 1.92, showing that, even without any form of scaling between the parameters, the same values can be obtained. This, compared with other such studies, indicates that time-of-flight neutron diffraction data can give structural information of a quality comparable to monochromatic neutron diffraction. The excellent correspondence between the thermal parameters derived separately from X-ray and neutron diffraction data gives confidence in the deconvolution of the thermal motion from the X-ray diffraction data, which is necessary for any study of a static electron density distribution.

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).

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.

The effect of sample position on the determination of triaxial stress by X-ray diffraction

1988 ◽  
Vol 21 (1) ◽  
pp. 38-41 ◽  
Author(s):  
R. H. Fenn ◽  
A. M. Jones
Keyword(s):  
Shear Stress ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Stress Components ◽  
Sample Position ◽  
Measured Strain ◽  
The Difference ◽  
Negative Sense

The determination of the full three-dimensional stress tensor in a specimen by X-ray diffraction requires that the strain be measured with the sample tilted in both a positive and a negative sense for different rotations of the sample in its own plane. The error introduced in the measured strain as a function of the position of the specimen relative to the X-ray diffractometer axis is investigated and it is shown that the negative tilt values are more sensitive to sample position than the positive tilt values. The determination of the shear stress components uses the difference between the measured strain at equivalent positive and negative tilts and hence it is shown that displacement of the sample could lead to incorrect deductions concerning the presence and magnitude of the shear stress components.

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.

Ribosome Structural Organization

1974 ◽  
Vol 32 ◽  
pp. 332-333
Author(s):  
James A. Lake
Keyword(s):  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Small Subunit ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Specific Antibodies ◽  
X Ray ◽  
E Coli ◽  
Complete Sequences

The understanding of ribosome structure has advanced considerably in the last several years. Biochemists have characterized the constituent proteins and rRNA's of ribosomes. Complete sequences have been determined for some ribosomal proteins and specific antibodies have been prepared against all E. coli small subunit proteins. In addition, a number of naturally occuring systems of three dimensional ribosome crystals which are suitable for structural studies have been observed in eukaryotes. Although the crystals are, in general, too small for X-ray diffraction, their size is ideal for electron microscopy.

Antiphase Boundaries in Ordered Ni3FE Crystals

1969 ◽  
Vol 27 ◽  
pp. 62-63
Author(s):  
Y. H. Liu
Keyword(s):  
Domain Size ◽  
Antiphase Domain ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hardening Mechanism ◽  
Superlattice Structure ◽  
Disordered Phase ◽  
Domain Boundaries ◽  
Atomic Scattering ◽  
The Difference

Ordered Ni3Fe crystals possess a LI2 type superlattice similar to the Cu3Au structure. The difference in slip behavior of the superlattice as compared with that of a disordered phase has been well established. Cottrell first postulated that the increase in resistance for slip in the superlattice structure is attributed to the presence of antiphase domain boundaries. Following Cottrell's domain hardening mechanism, numerous workers have proposed other refined models also involving the presence of domain boundaries. Using the anomalous X-ray diffraction technique, Davies and Stoloff have shown that the hardness of the Ni3Fe superlattice varies with the domain size. So far, no direct observation of antiphase domain boundaries in Ni3Fe has been reported. Because the atomic scattering factors of the elements in NijFe are so close, the superlattice reflections are not easily detected. Furthermore, the domain configurations in NioFe are thought to be independent of the crystallographic orientations.

Sign in / Sign up

Export Citation Format

Share Document