scholarly journals A non-mathematical introduction to the superspace description of modulated structures

2009 ◽  
Vol 65 (3) ◽  
pp. 249-268 ◽  
Author(s):  
Trixie Wagner ◽  
Andreas Schönleber
Keyword(s):  
Crystal Structure ◽  
Data Processing ◽  
Reciprocal Lattice ◽  
Molecular Compound ◽  
Modulated Structure ◽  
X Ray ◽  
Modulated Structures ◽  
Structure Solution ◽  
Superspace Description ◽  
Complete Process

The X-ray analysis of (6R,7aS)-6-(tert-butyl-dimethylsilanyloxy)-1-hydroxy-2-phenyl-5,6,7,7a-tetrahydropyrrolizin-3-one, C19H27NO3Si, revealed a diffraction pattern which is typical for modulated structures: strong Bragg peaks surrounded by weaker reflections which cannot be indexed with the same three reciprocal lattice vectors that are used to describe the strong peaks. For this class of crystal structures the concept of superspace has been developed which, however, for many crystallographers still constitutes a Gordian Knot. As a possible tool to cut this knot the crystal structure of the above-mentioned tetrahydropyrrolizinone derivative is presented as an illustrative example for handling and describing the modulated structure of a typical pharmaceutical (i.e. molecular) compound. Having established a working knowledge of the concepts and terminology of the superspace approach a concise and detailed description of the complete process of peak indexing, data processing, structure solution and structure interpretation is presented for the incommensurately modulated crystal structure of the above-mentioned compound. The superspace symmetry applied is P21(α0γ)0; the (incommensurate) q vector components at 100 K are α = 0.1422 (2) and γ = 0.3839 (8).

Modulated corrugations in the crystal structure of the superconductor CaAlSi

2006 ◽  
Vol 62 (5) ◽  
pp. 710-718 ◽  
Author(s):  
Karine M. Sparta ◽  
Ralf Müller ◽  
Michael Merz ◽  
Georg Roth ◽  
Peter Adelmann ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Thermal History ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Modulated Structure ◽  
X Ray ◽  
Modulated Phases ◽  
Modulated Structures ◽  
History Of

We report the crystal structure analyses of CaAlSi from single-crystal and powder X-ray diffraction and the existence of two commensurately modulated phases, a sixfold and a fivefold modulated structure. This polymorphism seems to be correlated to the thermal history of the sample. We describe both modulated structures using a three-dimensional and a (3 + 1)-dimensional formalism.

scholarly journals Optimization in S-SAD phasing - difference between solved and unsolved structure

2014 ◽  
Vol 70 (a1) ◽  
pp. C613-C613
Author(s):  
Jan Stránský ◽  
Tomáš Kovaľ ◽  
Lars Østergaard ◽  
Jarmila Dušková ◽  
Tereza Skálová ◽  
...  
Keyword(s):  
Data Processing ◽  
De Novo ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Sad Phasing ◽  
Optimal Values ◽  
Grant Agency ◽  
Intensity Reading

Development of X-ray diffraction technologies have made de novo phasing of protein structures by single-wavelength anomalous dispersion by sulphur (S-SAD) more common. As anomalous differences in the sulphur atomic factors are in the order of errors of measurement, careful intensity reading and data processing are crucial. S-SAD was used for de novo phasing of a small 12 kDa protein with 4 sulphur atoms per molecule at 2.3 Å, where the data did not enable a straightforward structure solution. Data processing was performed using XDS [1] and scaling using XSCALE. The sulphur substructure was determined by SHELXD [2] and phases were obtained from SHELXE [2]. Both algorithms strongly depend on input parameters and default values did not lead to the correct phases. Therefore a systematic search of optimal values of several parameters was used to find a solution. This method helped to confirm sulphur substructure and to differentiate the handedness of the solutions. Moreover, a script for comfortable conversion of SHELX outputs to MTZ format was developed, using programmes included in the CCP4 package [3]. The previously unsolvable protein structure was successfully resolved with the described procedure. This work was supported by the Grant Agency of the Czech Technical University in Prague, (SGS13/219/OHK4/3T/14), the Czech Science Foundation (P302/11/0855), project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.

New similarity index for crystal structure determination from X-ray powder diagrams

2005 ◽  
Vol 38 (6) ◽  
pp. 861-866 ◽  
Author(s):  
Detlef Walter Maria Hofmann ◽  
Ludmila Kuleshova
Keyword(s):  
Crystal Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Similarity Index ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
X Ray ◽  
Organic Pigments ◽  
Structure Solution ◽  
Similarity Indices

A new similarity index for automated comparison of powder diagrams is proposed. In contrast to traditionally used similarity indices, the proposed method is valid in cases of large deviations in the cell constants. The refinement according to this index closes the gap between crystal structure prediction and automated crystal structure determination. The opportunities of the new procedure have been demonstrated by crystal structure solution of un-indexed powder diagrams of some organic pigments (PY111, PR181 and Me-PR170).

Extended structures in copper(II) complexes with 4-hydroxypyridine-2,6-dicarboxylate and pyrimidine derivative ligands: X-ray crystal structure, solution and magnetic studies

2014 ◽  
Vol 418 ◽  
pp. 126-135 ◽  
Author(s):  
Masoud Mirzaei ◽  
Vito Lippolis ◽  
M. Carla Aragoni ◽  
Manoochehr Ghanbari ◽  
Mojtaba Shamsipur ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Pyrimidine Derivative ◽  
Magnetic Studies ◽  
X Ray ◽  
Structure Solution

scholarly journals SUPERFLIP– a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions

2007 ◽  
Vol 40 (4) ◽  
pp. 786-790 ◽  
Author(s):  
Lukáš Palatinus ◽  
Gervais Chapuis
Keyword(s):  
Computer Program ◽  
Crystal Structures ◽  
Diffraction Data ◽  
Periodic Structures ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Modulated Structures ◽  
Structure Solution ◽  
Matching Procedure ◽  
Arbitrary Dimensions

SUPERFLIPis a computer program that can solve crystal structures from diffraction data using the recently developed charge-flipping algorithm. It can solve periodic structures, incommensurately modulated structures and quasicrystals from X-ray and neutron diffraction data. Structure solution from powder diffraction data is supported by combining the charge-flipping algorithm with a histogram-matching procedure.SUPERFLIPis written in Fortran90 and is distributed as a source code and as precompiled binaries. It has been successfully compiled and tested on a variety of operating systems.

Crystal structure study of selected xanthine derivatives

2010 ◽  
Vol 43 (1) ◽  
pp. 163-167 ◽  
Author(s):  
W. Lasocha ◽  
B. Gaweł ◽  
A. Rafalska-Lasocha ◽  
M. Pawłowski ◽  
P. Talik ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Powder Diffraction ◽  
Structure Study ◽  
Asymmetric Unit ◽  
Pharmaceutical Samples ◽  
X Ray ◽  
Xanthine Derivatives ◽  
Structure Solution ◽  
Theophylline Derivatives

The crystal structures of two compounds belonging to a group of theophylline derivatives have been solved by X-ray powder diffraction methods. Despite the fact that these compounds seemed to be rather simple (23 atoms in an asymmetric unit), the preferred orientation and dominant zone problems created very serious obstacles in the investigations, even for the most modern powder diffraction methods. The crystal structure of the first compound, 8-phenylazoxanthine, C14H14N6O2, was finally solved from laboratory diffractometer data, while in the case of the second compound, 8-(3-bromobenzylidene)xanthine, C15H14N5O2Br, it was not possible to reliably index its diffraction pattern until data had been collected at the high-resolution powder diffractometer ID31 at the ESRF Grenoble. The serious problems encountered during anab initiocrystal structure solution from powder data of these pharmaceutical samples are described and discussed.

scholarly journals Crystal structure solution of an elusive polymorph of Dibenzylsquaramide

2013 ◽  
Vol 28 (S2) ◽  
pp. S470-S480 ◽  
Author(s):  
Anna Portell ◽  
Xavier Alcobé ◽  
Latévi M. Lawson Daku ◽  
Radovan Černý ◽  
Rafel Prohens
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structural Features ◽  
Powder Diffraction Data ◽  
Asymmetric Unit ◽  
X Ray ◽  
The Third ◽  
Group Assignment ◽  
Structure Solution

The crystal structure of the third polymorph of dibenzylsquaramide (Portell, A. et al., 2009), (fig. 1) has been determined from laboratory X-ray powder diffraction data by means of direct space methods using the computing program FOX. (Favre-Nicolin and Černý, 2002) The structure resolution has not been straightforward due to several difficulties on the indexing process and in the space group assignment. The asymmetric unit contains two different conformers, which has implied an additional difficulty during the Rietveld (Rietveld, 1969) refinement. All these issues together with particular structural features of disquaramides are discussed.

scholarly journals Kandungan Mineral dan Struktur Kristal Batu Sekis

2020 ◽  
Vol 4 (1) ◽  
pp. 24-30
Author(s):  
Muhamad Ragil Setiawan ◽  
Rahmat Nawi Siregar
Keyword(s):  
Crystal Structure ◽  
Data Processing ◽  
Mineral Content ◽  
Diffraction Method ◽  
Lattice Parameters ◽  
X Ray Diffraction ◽  
Rock Crystal ◽  
X Ray ◽  
Two Samples ◽  
Processing Information

This study aims to determine the mineral content and crystal structure of schist rocks in South Lampung. The method used in this research is the X-ray diffraction method to see the lattice parameters and the crystal structure of the schist rocks. Based on data processing, information was obtained that two main minerals were found, namely quartz and albite minerals. In conclusion, the Albit minerals found in the two samples of rock crystal schists in South Lampung have the same crystal structure and lattice parameters, while the quartz minerals from the two samples have different crystal structures and lattice parameters. Keywords: Lampung, Schis, XRD, Crystal Structure

scholarly journals Structure for the N-terminal domain of HCV glycoprotein E1

2014 ◽  
Vol 70 (a1) ◽  
pp. C1803-C1803
Author(s):  
Kamel El Omari ◽  
Oleg Iourin ◽  
Jan Kadlec ◽  
Geoff Sutton ◽  
Richard Fearn ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Model Building ◽  
Heavy Atom ◽  
Protein Fold ◽  
X Ray ◽  
Terminal Domain ◽  
Structure Solution ◽  
Phase Extension ◽  
Resolution Model ◽  
Covalently Linked

Single-wavelength anomalous dispersion of sulfur atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy atom incorporation or selenomethionine derivatization. Nevertheless this technique has been limited by the paucity of the signal at usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here we report the data collection and structure solution of the N-terminal domain of the ectodomain of Hepatitis C virus (HCV) E1, from crystals that diffracted very weakly. By combining the data from 32 crystals it was possible to solve the sulfur substructure and calculate initial maps at 7Å resolution, and after density modification and phase extension, using a higher resolution native dataset, to 3.5Å resolution, model building was achievable. The crystal structure of the N-terminal domain of reveals a complex network of covalently linked intertwined homodimers that do not harbor the expected truncated class II fusion protein fold.

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