scholarly journals How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological macromolecular crystal

2017 ◽  
Vol 50 (4) ◽  
pp. 1200-1207 ◽  
Author(s):  
Jason Porta ◽  
Jeff Lovelace ◽  
Gloria E. O. Borgstahl
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Real Life ◽  
Group Symmetry ◽  
Protein Crystal ◽  
3D Space ◽  
Structure Solution ◽  
Crystallographic Symmetry ◽  
Aperiodic Crystals ◽  
Periodic Crystal

Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and requireqvectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical crystallographers are fully described in Volume C ofInternational Tables for Crystallography. This text includes all types of crystallographic symmetry elements found in small-molecule crystals and can be difficult for structural biologists to understand and apply to their crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein crystal.

scholarly journals Dealing with Aperiodic Protein Crystal Structures

2014 ◽  
Vol 70 (a1) ◽  
pp. C778-C778
Author(s):  
Gloria Borgstahl
Keyword(s):  
Three Dimensional ◽  
Protein Crystal ◽  
Periodic Lattice ◽  
X Rays ◽  
Future Directions ◽  
Space Group ◽  
3D Space ◽  
Structure Solution ◽  
Quasi Crystals ◽  
Aperiodic Crystals

Protein crystals can be aperiodic. They will diffract X-rays, and are therefore a crystal, but their diffraction is not periodic. This means that their diffraction pattern cannot be simply be indexed by a typical three-dimensional unit cell and space group. Aperiodic crystals include "quasi-crystals" as well as "modulated" crystals. In the latter case, the modulation can be positional or occupational and these modulations can be incommensurate with the normal periodic lattice [1]. An overview of aperiodic protein crystal diffraction will be presented with examples. The discussion will then focus on the characteristics of incommensurately modulated crystals followed by a more detailed discussion of how to solve these crystals. The following details of structure solution will be presented: (1) data collection perils; (2) specialized diffraction data processing in (3+1)D space using a q-vector [2]; (3) how to get an approximation of the structure in 3D space; (4) the assignment of the (3+1)D space group; and the ultimate (5) crystallographic refinement in superspace[3]. Future directions and needs will be discussed.

scholarly journals Crystal structure of the coordination polymer [FeIII2{PtII(CN)4}3]

2015 ◽  
Vol 71 (1) ◽  
pp. i1-i2
Author(s):  
Maksym Seredyuk ◽  
M. Carmen Muñoz ◽  
José A. Real ◽  
Turganbay S. Iskenderov
Keyword(s):  
Crystal Structure ◽  
Coordination Polymer ◽  
Point Group ◽  
Three Dimensional ◽  
Title Complex ◽  
Group Symmetry ◽  
Point Group Symmetry ◽  
Rotation Axes ◽  
Square Planar ◽  
Cyanide Ligands

The title complex, poly[dodeca-μ-cyanido-diiron(III)triplatinum(II)], [FeIII2{PtII(CN)4}3], has a three-dimensional polymeric structure. It is built-up from square-planar [PtII(CN)4]2−anions (point group symmetry 2/m) bridging cationic [FeIIIPtII(CN)4]+∞layers extending in thebcplane. The FeIIatoms of the layers are located on inversion centres and exhibit an octahedral coordination sphere defined by six N atoms of cyanide ligands, while the PtIIatoms are located on twofold rotation axes and are surrounded by four C atoms of the cyanide ligands in a square-planar coordination. The geometrical preferences of the two cations for octahedral and square-planar coordination, respectively, lead to a corrugated organisation of the layers. The distance between neighbouring [FeIIIPtII(CN)4]+∞layers corresponds to the lengtha/2 = 8.0070 (3) Å, and the separation between two neighbouring PtIIatoms of the bridging [PtII(CN)4]2−groups corresponds to the length of thecaxis [7.5720 (2) Å]. The structure is porous with accessible voids of 390 Å3per unit cell.

scholarly journals Crystal structure of langbeinite-related Rb0.743K0.845Co0.293Ti1.707(PO4)3

2015 ◽  
Vol 71 (3) ◽  
pp. 251-253 ◽  
Author(s):  
Nataliia Yu. Strutynska ◽  
Marina A. Bondarenko ◽  
Ivan V. Ogorodnyk ◽  
Vyacheslav N. Baumer ◽  
Nikolay S. Slobodyanik
Keyword(s):  
Crystal Structure ◽  
High Temperature ◽  
Point Group ◽  
Three Dimensional ◽  
Type Structure ◽  
Group Symmetry ◽  
Site Symmetry ◽  
Point Group Symmetry ◽  
Crystallization Method ◽  
Temperature Crystallization

Potassium rubidium cobalt(II)/titanium(IV) tris(orthophosphate), Rb0.743K0.845Co0.293Ti1.707(PO4)3, has been obtained using a high-temperature crystallization method. The obtained compound has a langbeinite-type structure. The three-dimensional framework is built up from mixed-occupied (Co/TiIV)O6octahedra (point group symmetry .3.) and PO4tetrahedra. The K+and Rb+cations are statistically distributed over two distinct sites (both with site symmetry .3.) in the large cavities of the framework. They are surrounded by 12 O atoms.

scholarly journals Three-dimensional crystal structure of novel aluminophosphate PST-5 solved using a powder charge flipping method

RSC Advances ◽  
2017 ◽  
Vol 7 (61) ◽  
pp. 38631-38638 ◽  
Author(s):  
Shuai Chang ◽  
Hoi-Gu Jang ◽  
Kwan-Young Lee ◽  
Sung June Cho
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Powder Charge ◽  
Structure Solution ◽  
Dimensional Crystal

Novel PST-5 which resists structure solution has been solved using a powder charge flipping method.

Crystallization and structure solution of p53 (residues 326–356) by molecular replacement using an NMR model as template

1998 ◽  
Vol 54 (1) ◽  
pp. 86-89 ◽  
Author(s):  
Peer R. E. Mittl ◽  
Patrick Chène ◽  
Markus G. Grütter
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
Additional Information ◽  
Nmr Structures ◽  
Replacement Method ◽  
Tetramerization Domain ◽  
Structure Solution ◽  
Molecular Replacement Method

The molecular replacement method is a powerful technique for crystal structure solution but the use of NMR structures as templates often causes problems. In this work the NMR structure of the p53 tetramerization domain has been used to solve the crystal structure by molecular replacement. Since the rotation- and translation-functions were not sufficiently clear, additional information about the symmetry of the crystal and the protein complex was used to identify correct solutions. The three-dimensional structure of residues 326–356 was subsequently refined to a final R factor of 19.1% at 1.5 Å resolution.

EDMA: a computer program for topological analysis of discrete electron densities

2012 ◽  
Vol 45 (3) ◽  
pp. 575-580 ◽  
Author(s):  
Lukáš Palatinus ◽  
Siriyara Jagannatha Prathapa ◽  
Sander van Smaalen
Keyword(s):  
Computer Program ◽  
Electron Density ◽  
Critical Points ◽  
Topological Analysis ◽  
Three Dimensional ◽  
Real Space ◽  
Principal Curvatures ◽  
Electron Densities ◽  
Structure Solution ◽  
Aperiodic Crystals

EDMAis a computer program for topological analysis of discrete electron densities according to Bader's theory of atoms in molecules. It locates critical points of the electron density and calculates their principal curvatures. Furthermore, it partitions the electron density into atomic basins and integrates the volume and charge of these atomic basins.EDMAcan also assign the type of the chemical element to atomic basins based on their integrated charges. The latter feature can be used for interpretation ofab initioelectron densities obtained in the process of structure solution. A particular feature ofEDMAis that it can handle superspace electron densities of aperiodic crystals in arbitrary dimensions.EDMAfirst generates real-space sections at a selected set of phases of the modulation wave, and subsequently analyzes each section as an ordinary three-dimensional electron density. Applications ofEDMAto model electron densities have shown that the relative accuracy of the positions of the critical points, the electron densities at the critical points and the Laplacian is of the order of 10−4or better.

scholarly journals (NH4)Mg(HSO4)(SO4)(H2O)2 and NaSc(CrO4)2(H2O)2, two crystal structures comprising kröhnkite-type chains, and the temperature-induced phase transition (NH4)Mg(HSO4)(SO4)(H2O)2\rightleftharpoons (NH4)MgH(SO4)2(H2O)2

2021 ◽  
Vol 77 (3) ◽  
pp. 144-151
Author(s):  
Matthias Weil ◽  
Uwe Kolitsch
Keyword(s):  
Crystal Structure ◽  
Phase Transition ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Room Temperature ◽  
Classification Scheme ◽  
Three Dimensional ◽  
Structure Type ◽  
Group Symmetry ◽  
Water Molecules

The crystal structure of the mineral kröhnkite, Na2Cu(SO4)2(H2O)2, contains infinite chains composed of [CuO4(OH2)2] octahedra corner-linked with SO4 tetrahedra. Such or similar tetrahedral–octahedral `kröhnkite-type' chains are present in the crystal structures of numerous compounds with the composition AnM(XO4)2(H2O)2. The title compounds, (NH4)Mg(HSO4)(SO4)(H2O)2, ammonium magnesium hydrogen sulfate sulfate dihydrate, and NaSc(CrO4)2(H2O)2, sodium scandium bis(chromate) dihydrate, are members of the large family with such kröhnkite-type chains. At 100 K, (NH4)Mg(HSO4)(SO4)(H2O)2 has an unprecedented triclinic crystal structure and contains [MgO4(OH2)2] octahedra linked by SO3(OH) and SO4 tetrahedra into chains extending parallel to [\overline{1}10]. Adjacent chains are linked by very strong hydrogen bonds between SO3(OH) and SO4 tetrahedra into layers parallel to (111). Ammonium cations and water molecules connect adjacent layers through hydrogen-bonding interactions of medium-to-weak strength into a three-dimensional network. (NH4)Mg(HSO4)(SO4)(H2O)2 shows a reversible phase transition and crystallizes at room temperature in structure type E in the classification scheme for structures with kröhnkite-type chains, with half of the unit-cell volume for the resulting triclinic cell, and with disordered H atoms of the ammonium tetrahedron and the H atom between two symmetry-related sulfate groups. IR spectroscopic room-temperature data for the latter phase are provided. Monoclinic NaSc(CrO4)2(H2O)2 adopts structure type F1 in the classification scheme for structures with kröhnkite-type chains. Here, [ScO4(OH2)2] octahedra (point group symmetry \overline{1}) are linked by CrO4 tetrahedra into chains parallel to [010]. The Na+ cations (site symmetry 2) have a [6 + 2] coordination and connect adjacent chains into a three-dimensional framework that is consolidated by medium–strong hydrogen bonds involving the water molecules. Quantitative structural comparisons are made between NaSc(CrO4)2(H2O)2 and its isotypic NaM(CrO4)2(H2O)2 (M = Al and Fe) analogues.

scholarly journals Crystal structure of Ag2(μ-SCN)2(NH3)4

2016 ◽  
Vol 72 (7) ◽  
pp. 881-883 ◽  
Author(s):  
Thomas G. Müller ◽  
Florian Kraus
Keyword(s):  
Crystal Structure ◽  
Liquid Ammonia ◽  
Point Group ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Hydrogen Bonding Interactions ◽  
Dimensional Network ◽  
Binuclear Molecule ◽  
Thiocyanate Ligand ◽  
Argentophilic Interactions

Di-μ-thiocyanato-bis[diamminesilver(I)], [Ag2(μ-SCN)2(NH3)4], was synthesized by the reaction of AgSCN with anhydrous liquid ammonia. In the binuclear molecule, the AgIatom is coordinated by two ammine ligands and the S atom of one thiocyanate ligand. Two of these [Ag(SCN)(NH3)2] units are bridged by the S atoms of the thiocyanate anions at longer distances, leading to a dimer with point group symmetryC2. The distance between the AgIatoms in the dimer is at 3.0927 (6) Å within the range of argentophilic interactions. The crystal structure displays N—H...N and N—H...S hydrogen-bonding interactions that build up a three-dimensional network.

Refinement of the crystal structure of zirconyl chloride octahydrate

1968 ◽  
Vol 46 (22) ◽  
pp. 3491-3497 ◽  
Author(s):  
Thomas C. W. Mak
Keyword(s):  
Crystal Structure ◽  
Axial Symmetry ◽  
Experimental Error ◽  
Least Squares Method ◽  
Point Group ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Point Group Symmetry ◽  
Zirconium Atom ◽  
Zirconyl Chloride

The crystal structure of zirconyl chloride octahydrate, ZrOCl2•8H2O, has been refined by the least-squares method with new three-dimensional data. Existence of the [Zr4(OH)8(H2O)16]8+ tetranuclear complex has been confirmed. However, the coordination polyhedron about each zirconium atom differs considerably from the D4d antiprismatic geometry reported previously. It is, in fact, more closely related to the D2d dodecahedron, and has twofold axial symmetry within the limits of experimental error. Mean bond lengths in the [Zr4(OH)8(H2O)16]8+ complex, which approximates closely to D2d point-group symmetry, are: Zr—OH (bridging) = 2.142 ± 0.019 Å and Zr—OH2 (terminal) = 2.272 ± 0.032 Å.

scholarly journals Crystal structure of high-spin tetraaquabis(2-chloropyrazine-κN4)iron(II) bis(4-methylbenzenesulfonate)

2015 ◽  
Vol 71 (7) ◽  
pp. 776-778
Author(s):  
Bohdan O. Golub ◽  
Sergii I. Shylin ◽  
Sebastian Dechert ◽  
Maria L. Malysheva ◽  
Il`ya A. Gural`skiy
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
High Spin ◽  
Supramolecular Structure ◽  
Complex Cation ◽  
Point Group ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Point Group Symmetry ◽  
Π Interactions

The title salt, [FeII(C4H3ClN2)2(H2O)4](C7H7O3S)2, contains a complex cation with point group symmetry 2/m. The high-spin FeIIcation is hexacoordinated by four symmetry-related water and twoN-bound 2-chloropyrazine molecules in atransarrangement, forming a distorted FeN2O4octahedron. The three-dimensional supramolecular structure is supported by intermolecular O—H...O hydrogen bonds between the complex cations and tosylate anions, and additional π–π interactions between benzene and pyrazine rings. The methyl H atoms of the tosylate anion are equally disordered over two positions.

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