XAFS studies of nitrogenase: the MoFe and VFe proteins and the use of crystallographic coordinates in three-dimensional EXAFS data analysis

2002 ◽  
Vol 10 (1) ◽  
pp. 71-75 ◽  
Author(s):  
Richard W. Strange ◽  
Robert R. Eady ◽  
David Lawson ◽  
S. Samar Hasnain
Keyword(s):  
Crystal Structure ◽  
Data Analysis ◽  
Klebsiella Pneumoniae ◽  
Crystal Structures ◽  
Excellent Agreement ◽  
Coordination Sphere ◽  
Three Dimensional ◽  
Protein Crystal ◽  
Mofe Protein ◽  
Distance Restraints

This paper reports a three-dimensional EXAFS refinement of the Mo coordination sphere of the FeMoco cluster of the dithionite-reduced MoFe protein fromKlebsiella pneumoniaenitrogenase (Kp1) using the 1.6 Å-resolution crystallographic coordinates. At this resolution, the positions of the heavy (Fe and S) atoms of the cluster are well determined and there is excellent agreement between the crystallographic and EXAFS models. However, the lighter homocitrate and histidine ligands are poorly determined in the crystal structure, and it is shown that the application of EXAFS-derived distance restraints during the early stages of crystallographic refinement provides a means of substantially improving (by ∼0.1 Å) the final crystallographic model. The consistency of the EXAFS analysis with the crystallographic information in this case justifies applications of EXAFS to cases where protein crystal structures are absent. Thus, the VFe protein of V-nitrogenase has been shown by EXAFS to possess a V-atom site catalytically similar to the well characterized MoFe-nitrogenases, with V replacing Mo.

The crystal structure of kalsilite, KAlSiO4

1965 ◽  
Vol 35 (272) ◽  
pp. 588-595 ◽  
Author(s):  
A. J. Perrotta ◽  
J. V. Smith
Keyword(s):  
Crystal Structure ◽  
Oxygen Atom ◽  
Crystal Structures ◽  
Bond Angle ◽  
Three Dimensional ◽  
Full Matrix ◽  
Ideal Position ◽  
Wide Range ◽  
The Ideal

SummaryA full-matrix, three-dimensional refinement of kalsilite, KAlSi04 (hexagonal, a 5·16, c 8.69 Å, P6a), shows that the silicon and aluminium atoms are ordered. The respective tetrahedral distances of 1·61 and 1·74 Å agree with values of 1·61 and 1·75 Å taken to be typical of framework structures. As in nepheline, an oxygen atom is statistically distributed over three sites displaced 0·25 Å from the ideal position on a triad axis. This decreases the bond angle from 180° to 163° in conformity with observations on some other crystal structures. The potassiumoxygen distances of 2·77, 2·93, and 2·99 Å are consistent with the wide range normally found for this weakly bonded atom.

scholarly journals Caesium tetramethylammonium dodecahydrido-closo-dodecaborate monohydrate

IUCrData ◽  
2016 ◽  
Vol 1 (2) ◽  
Author(s):  
Ioannis Tiritiris ◽  
Thomas Schleid
Keyword(s):  
Crystal Structure ◽  
Water Molecule ◽  
Coordination Sphere ◽  
Three Dimensional ◽  
Double Salt ◽  
Asymmetric Unit ◽  
Dihydrogen Bonds ◽  
Dimensional Network

In the crystal structure of the hydrated double salt, Cs+·[N(CH3)4]+·[B12H12]2−·H2O, the asymmetric unit contains one caesium and one tetramethylammonium cation, one dodecahydrido-closo-dodecaborate anion and one water molecule. The Cs+cation is coordinated tetrahedrally by four [B12H12]2−clusters, with the water molecule completing the coordination sphere. The tetramethylammonium cation is surrounded distorted octahedrally by six [B12H12]2−anions. The crystal structure is stabilized by a three-dimensional network of O—H...H—B and C—H...H—B dihydrogen bonds.

Crystal chemistry of zirconosilicates and their analogs: topological classification of MT frameworks and suprapolyhedral invariants

2002 ◽  
Vol 58 (2) ◽  
pp. 198-218 ◽  
Author(s):  
G. D. Ilyushin ◽  
V. A. Blatov
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Crystal Chemistry ◽  
Three Dimensional ◽  
Geometrical Interpretation ◽  
Topological Classification ◽  
Hierarchical Analysis ◽  
Framework Structure ◽  
Coordination Spheres

The first attempt is undertaken to consider systematically topological structures of zirconosilicates and their analogs (60 minerals and 34 synthetic phases), where the simplest structure units are MO6 octahedra and TO4 tetrahedra united by vertices ([TO4]:[MO6] = 1:1–6:1). A method of analysis and classification of mixed three-dimensional MT frameworks by topological types with coordination sequences {N k } is developed, which is based on the representation of crystal structure as a finite `reduced' graph. The method is optimized for the frameworks of any composition and complexity and implemented within the TOPOS3.2 program package. A procedure of hierarchical analysis of MT-framework structure organization is proposed, which is based on the concept of polyhedral microensemble (PME) being a geometrical interpretation of coordination sequences of M and T nodes. All 12 theoretically possible PMEs of MT 6 polyhedral composition are considered where T is a separate and/or connected tetrahedron. Using this methodology the MT frameworks in crystal structures of zirconosilicates and their analogs were analyzed within the first 12 coordination spheres of M and T nodes and related to 41 topological types. The structural correlations were revealed between rosenbuschite, lavenite, hiortdahlite, woehlerite, siedozerite and the minerals of the eudialyte family.

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 structures of chlorido[dihydroxybis(1-iminoethoxy)]arsanido-κ3 N,As,N′]platinum(II) and of a polymorph of chlorido[dihydroxybis(1-iminopropoxy)arsanido-κ3 N,As,N′]platinum(II)

2020 ◽  
Vol 76 (2) ◽  
pp. 180-185
Author(s):  
Nina R. Marogoa ◽  
D.V. Kama ◽  
Hendrik G. Visser ◽  
M. Schutte-Smith
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Donor Ligands ◽  
Intermolecular Hydrogen Bonding ◽  
Π Interactions ◽  
Hydrogen Bonding Interactions ◽  
Oxygen Donor ◽  
Dimensional Network

Each central platinum(II) atom in the crystal structures of chlorido[dihydroxybis(1-iminoethoxy)arsanido-κ3 N,As,N′]platinum(II), [Pt(C4H10AsN2O4)Cl] (1), and of chlorido[dihydroxybis(1-iminopropoxy)arsanido-κ3 N,As,N′]platinum(II), [Pt(C6H14AsN2O4)Cl] (2), is coordinated by two nitrogen donor atoms, a chlorido ligand and to arsenic, which, in turn, is coordinated by two oxygen donor ligands, two hydroxyl ligands and the platinum(II) atom. The square-planar and trigonal–bipyramidal coordination environments around platinum and arsenic, respectively, are significantly distorted with the largest outliers being 173.90 (13) and 106.98 (14)° for platinum and arsenic in (1), and 173.20 (14)° and 94.20 (9)° for (2), respectively. One intramolecular and four classical intermolecular hydrogen-bonding interactions are observed in the crystal structure of (1), which give rise to an infinite three-dimensional network. A similar situation (one intramolecular and four classical intermolecular hydrogen-bonding interactions) is observed in the crystal structure of (2). Various π-interactions are present in (1) between the platinum(II) atom and the centroid of one of the five-membered rings formed by Pt, As, C, N, O with a distance of 3.7225 (7) Å, and between the centroids of five-membered (Pt, As, C, N, O) rings of neighbouring molecules with distances of 3.7456 (4) and 3.7960 (6) Å. Likewise, weak π-interactions are observed in (2) between the platinum(II) atom and the centroid of one of the five-membered rings formed by Pt, As, C, N, O with a distance of 3.8213 (2) Å, as well as between the Cl atom and the centroid of a symmetry-related five-membered ring with a distance of 3.8252 (12) Å. Differences between (2) and the reported polymorph [Miodragović et al. (2013). Angew. Chem. Int. Ed. 52, 10749–10752] are discussed.

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.

Syntheses and Crystal Structures of the Bromide-derivatized Lanthanoid(III) Ortho-Oxomolybdates(VI) LnBr[MoO4] (Ln = Pr, Nd, Sm, Gd– Lu)

2013 ◽  
Vol 68 (5-6) ◽  
pp. 616-624 ◽  
Author(s):  
Tanja Schustereit ◽  
Harald Henning ◽  
Thomas Schleid ◽  
Ingo Hartenbach
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Coordination Number ◽  
Coordination Sphere ◽  
Space Group ◽  
Structural Arrangement ◽  
Common Structure ◽  
Coordination Spheres ◽  
The Common ◽  
Oxygen Atoms

The lanthanoid(III) bromide ortho-oxomolybdates(VI) LnBr[MoO4] (Ln = Pr, Nd, Sm, Gd - Lu) crystallize triclinically in the space group P1 (a=686 - 689, b=713 - 741, c=1066 - 1121 pm, a =103 - 106, b =107 - 108, g = 92 - 95°) with Z =4. The crystal structure contains two crystallographically distinguishable Ln3+ cations, each one with a coordination number of seven plus one. (Ln1)3+ is surrounded by three bromide and four plus one oxide anions, while for (Ln2)3+ just one bromide and six plus one oxide anions belong to the coordination sphere. Considering the smallest lanthanoids, however, the distances to the farthest anions increase so much that their contribution to the coordination spheres becomes negligible in both cases. The polyhedra around (Ln1)3+ are connected to each other via common edges, which consist of two crystallographically identical Br- anions (Br1). Furthermore, the common structure of the LnBr[MoO4] series contains two crystallographically different, discrete [MoO4]2- ortho-oxomolybdate(VI) tetrahedra. Two plus one oxygen atoms of each [(Mo1)O4]2- unit are used to interconnect the polyhedra around (Ln1)3+ and (Ln2)3+ together with one Br- anion (Br2). The connection between two polyhedra around (Ln2)3+ is generated exclusively by two plus one oxygen atoms of two [(Mo2)O4]2- anions. The complete structural arrangement can be considered as a bundle of primitively packed 1¥{LnBr[MoO4]} chains with two alternating motifs of linkage, which are running parallel along [012].

Crystal Structures and Thermal Behavior of Alkaline Earth Tricyanomethanides

2008 ◽  
Vol 63 (3) ◽  
pp. 285-288 ◽  
Author(s):  
Karl E. Bessler ◽  
Claudia C. Gatto ◽  
Lincoln L. Romualdo ◽  
Javier A. Ellena ◽  
Maria J. de A. Sales
Keyword(s):  
Crystal Structure ◽  
Coordination Polymer ◽  
Thermal Behavior ◽  
Crystal Structures ◽  
Alkaline Earth ◽  
Three Dimensional ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Interpenetrating Networks ◽  
X Ray

The alkaline earth tricyanomethanides Mg(tcm)2 · 2H2O, Ca(tcm)2, Sr(tcm)2 ・H2O and Ba(tcm)2 · 2H2O were prepared from aqueous solutions of the respective chlorides and silver tricyanomethanide. Their IR spectra and thermal behavior are described. The crystal structures of Ca(tcm)2 and Ba(tcm)2 · 2H2O were determined by single crystal X-ray diffraction. The structure of Ca(tcm)2 is of the type found for several transition metal tricyanomethanides [1], containing two independent interpenetrating networks. Ba(tcm)2 · 2H2O has a unique crystal structure corresponding to a three-dimensional coordination polymer with nine fold coordinated Ba atoms connected by water molecules and tricyanomethanide anions.

Crystal Structure and Vibrational Behaviour of Tetraaqua-di(nicotinamide)M(II)-Saccharinates, with M(II) = Co, Ni, Zn

2002 ◽  
Vol 57 (6) ◽  
pp. 657-660 ◽  
Author(s):  
Eduardo E. Castellano ◽  
Oscar E. Piro ◽  
Beatriz S. Parajón-Costa ◽  
Enrique J. Baran
Keyword(s):  
Crystal Structure ◽  
Ir Spectra ◽  
Single Crystal ◽  
Crystal Structures ◽  
Coordination Sphere ◽  
Water Molecules ◽  
Triclinic Space Group ◽  
X Ray ◽  
Octahedral Environment ◽  
Coordinated Water

AbstractThe crystal structures of [M(nic)2 (H2O)4](sac)2 (nic = nocotinamide; sac = saccharinate anion) with M = Co(II), Ni(II) and Zn(II), have been determined at 116 K by single-crystal X-ray diffractometry. The compounds crystallize in the triclinic space group P1̅ with Z = 1, and the M(II) cations present a slightly distorted MN2O4 octahedral environment, with equatorially coordinated water molecules and axially pyridine N-bound nicotinamide ligands. The saccharinate anions act as counteranions, and are not part of the first coordination sphere. Some comparisons with related structures have been made and the most important features of their IR spectra discussed.

scholarly journals Crystal structures of isomeric 3,5-dichloro-N-(2,3-dimethylphenyl)benzenesulfonamide, 3,5-dichloro-N-(2,6-dimethylphenyl)benzenesulfonamide and 3,5-dichloro-N-(3,5-dimethylphenyl)benzenesulfonamide

2017 ◽  
Vol 73 (5) ◽  
pp. 673-677 ◽  
Author(s):  
K. Shakuntala ◽  
S. Naveen ◽  
N. K. Lokanath ◽  
P. A. Suchetan
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Molecular Conformation ◽  
Three Dimensional ◽  
Aromatic Rings ◽  
One Dimensional ◽  
Π Interactions ◽  
Hydrogen Bonded

The crystal structures of three isomeric compounds of formula C14H13Cl2NO2S, namely 3,5-dichloro-N-(2,3-dimethylphenyl)-benzenesulfonamide (I), 3,5-dichloro-N-(2,6-dimethylphenyl)benzenesulfonamide (II) and 3,5-dichloro-N-(3,5-dimethylphenyl)benzenesulfonamide (III) are described. The molecules of all the three compounds are U-shaped with the two aromatic rings inclined at 41.3 (6)° in (I), 42.1 (2)° in (II) and 54.4 (3)° in (III). The molecular conformation of (II) is stabilized by intramolecular C—H...O hydrogen bonds and C—H...π interactions. The crystal structure of (I) features N—H...O hydrogen-bondedR22(8) loops interconnectedvia C(7) chains of C—H...O interactions, forming a three-dimensional architecture. The structure also features π–π interactions [Cg...Cg= 3.6970 (14) Å]. In (II), N—H...O hydrogen-bondedR22(8) loops are interconnectedviaπ–π interactions [intercentroid distance = 3.606 (3) Å] to form a one-dimensional architecture running parallel to theaaxis. In (III), adjacentC(4) chains of N—H...O hydrogen-bonded molecules running parallel to [010] are connectedviaC—H...π interactions, forming sheets parallel to theabplane. Neighbouring sheets are linkedviaoffset π–π interactions [intercentroid distance = 3.8303 (16) Å] to form a three-dimensional architecture.

Sign in / Sign up

Export Citation Format

Share Document