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An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Ten programs for calculating cell parameters from single crystal electron diffraction patterns are presented. Most of the programs, written for use with a programmable desk calculator, are also applicable to X-ray diffraction work. The programs can be used to calculate d-spacings from electron diffraction plate measurements, and to determine cell data (including interplanar angles and zone angles) for all crystal systems. A program for rhombohedral-hexagonal conversions and one for matching crystal data from standards with apparent crystal parameters found in diffraction patterns are included. Because they allow rapid determination of data not present in X-ray listings or elsewhere in the literature, the programs facilitate identification of unknowns.
We have continued our long-term project using X-ray diffraction to characterize a wide range of extraterrestrial samples. The stationary sample method with polychromatic X-rays is advantageous because the irradiated area of the sample is always same and fixed, meaning that all diffraction spots occur from the same area of the sample, however, unit cell parameters cannot be directly obtained by this method though they are very important for identification of mineral and for determination of crystal structures. In order to obtain the cell parameters even in the case of the sample stationary method, we apply energy scanning of a micro-beam of monochromatic SR at SPring-8.
The synthesis of new materials is the lifeline of solid-state science, and it continues to offer us unique opportunities for testing various theoretical formulations and models on a practical material. Such an avenue, therefore, provides a breeding ground for technological innovations and advancements that can completely revolutionize our world. Here, we report the results of our exploratory syntheses in the Yb–Cd–Sb compositional space that lead to the identification of two new Zintl antimonides, namely, Yb10CdSb9 and Yb14CdSb11. Their crystal structures were established via single-crystal X-ray diffraction methods; the basic electronic and transport properties of the new materials were also characterized. Yb10CdSb9 crystallizes in a disordered variant of the tetragonal Ca10LiMgSb9 structure type with unit cell parameters a = 11.8473(8) Å and c = 17.1302(12) Å (space group P42/mnm). Yb14CdSb11 crystallizes in the tetragonal Ca14AlSb11 structure type with unit cell parameters: a = 16.605(3) Å and c = 12.144(7) Å (space group I41/acd). Although the structures of both compounds can be rationalized within the framework of the Zintl formalism, based on the partitioning of the valence electrons in the much disordered Yb10CdSb9 phase, the charge is indicative of a slightly electron-rich composition. Electronic structure calculations in both cases support the notion of intrinsic semiconductor behavior, as expected for a Zintl phase. The temperature dependence of the electrical resistivity of a single crystal of Yb10CdSb9 is in line with that, and the evolution of the Seebeck coefficient indicates an electron-dominated transport mechanism, and a respectable power factor of 0.71 μW/cm K2 at 460 K can be calculated for Yb10CdSb9. The electrical resistivity of Yb14CdSb11, however, evolves in a semimetallic manner, which could suggest an overdoped sample or degenerate semiconducting behavior.
Six potassium rare-earth molybdates KRE(MoO 4 ) 2 (RE = Tb, Dy, Ho, Er, Yb, and Lu) were synthesized by flux-assisted growth in K 2 Mo 3 O 10 . The crystal structures were determined using single-crystal X-ray diffraction data. The synthesized molybdates crystallize with the orthorhombic Pbcn space group (No. 60). Trendlines for unit-cell parameters were calculated using data from the current study. The unit-cell parameters a and c increase linearly whereas b decreases with larger RE cations, based on crystal radii. The unit-cell volumes increase linearly and the densities decrease linearly with larger RE cations. The average distances between the RE cations and the nearest O atoms increase with larger cations whereas the average distances of Mo—O and K—O do not show specific trends.
Dehydrolipoamide dehydrogenase (E3; dihydrolipoan-tide:NAD+ oxidoreductase, EC 1.8.1.4) is a common catalytic component found in pyruvate dehydrogenase complex, alpha-ketoglutarate dehydrogenase complex, and branched-chain cc-keto acid dehydrogenase complex. E3 is also a component (referred to as L protein) of the glycine cleavage system in bacterial metabolism (2). Active E3 forms a homodimer with four distinctive subdomain structures (FAD binding, NAD+ binding, central and interface domains) with non-covalently but tightly bound FAD in the holoenzyme. Deduced amino acids from cloned full-length human E3 gene showed a total of 509 amino acids with a leader sequence (N-terminal 35 amino acids) that is excised (mature form) during transportation of expressed E3 into mitochondria membrane. So far, three-dimensional structure of human E3 has not been reported. Our effort to achieve the elucidation of the X-ray crystal structure of human E3 will be presented. Recombinant pPROEX-1 expression vector (from GIBCO BRL Life Technologies) having the human E3 gene without leader sequence was constructed by Polymerase Chain Reaction (PCR) and subsequent ligation, and cloned in E.coli XL1-Blue by transformation. Since pPROEX-1 vector has an internal His-tag (six histidine peptide) located at the upstream region of a multicloning site, one-step affinity purification of E3 using nickelnitriloacetic acid (Ni-NTA) agarose resin, which has a strong affinity to His-tag, was feasible. Also a seven-amino-acid spacer peptide and a recombinant tobacco etch virus protease recognition site (seven amino acids peptide) found between His-tag and first amino acid of expressed E3 facilitated the cleavage of His-tag from E3 after the affinity purification. By IPTG induction, ca. 15 mg of human E3 (mature form) was obtained from 1L LB culture with overnight incubation at 25C. Over 98% of purity of E3 from one-step Ni-NTA agarose affinity purification was confirmed by SDS-PAGE analysis. For crystallization, E3 samples were prepared with and without His-tag. To minimize the aggregation of E3, apo- and holo- forms of E3s were tested, as well as a mutated E3. Dynamic light scattering measurements revealed that the E3 preparations without His-tag and substrate are highly monodispersive with regard to homodimers. Consequent crystallization trials of this E3 preparation led to single crystals of E3 grown by the vapor diffusion method. Crystals were obtained within a few days from solution containing poly (ethylene glycol) monomethyl ether 5000 as a precipitant. Autoindexing and integration of the X-ray diffraction data showed that E3 crystals belong to an orthorhombic system with unit cell parameters a-- 123. 1, b= 165.3 and c=214.3A. Further optimization of protein preparation and crystallization experiments for the structural determination will be discussed.
Human pyruvate dehydrogenase (E1) is a component enzyme of the pyruvate dehydrogenase complex. The enzyme catalyzes the irreversible decarboxylation of pyruvic acid and the rate-limiting reductive acetylation of the lipoyl moiety linked to the dihydrolipoamide acetyltransferase component of the pyruvate dehydrogenase complex. E1 is an alpha(2)beta(2) tetramer ( approximately 154 kDa). Crystals of this recombinant enzyme have been grown in polyethylene glycol 3350 using a vapor-diffusion method at 295 K. The crystals are characterized as orthorhombic, space group P2(1)2(1)2(1), with unit-cell parameters a = 64.2, b = 126.9, c = 190.2 A. Crystals diffracted to a minimum d spacing of 2.5 A. The asymmetric unit contains one alpha(2)beta(2) tetrameric E1 assembly; self-rotation function analysis showed a pseudo-twofold symmetry relating the two alphabeta dimers.
Abstract Here we have performed single-crystal X-ray diffraction (SCXRD) experiments on two high-quality crystal platelets of (Al,Fe)-bearing bridgmanite (Mg0.88Fe0.0653+Fe0.0352+Al0.03)(Al0.11Si0.90)O3 (Fe10-Al14-Bgm) up to 64.6(6) GPa at room temperature in a Boehler-Almax type diamond-anvil cell. Refinements on the collected SCXRD patterns reveal reliable structural information of single-crystal Fe10-Al14-Bgm, including unit-cell parameters, atomic coordinates, and anisotropic displacement parameters. Together with Mössbauer and electron microprobe analyses, our best single-crystal refinement model indicates that the sample contains ~6.5 mol% Fe3+, 3.5 mol% Fe2+, and 3 mol% Al3+ in the large pseudo-dodecahedral site (A site), and ~11 mol% Al3+ in the small octahedral site (B site). This may indicate that Al3+ in bridgmanite preferentially occupies the B site. Our results show that the compression of Fe10-Al14-Bgm with pressure causes monotonical decreases in the volumes of AO12 pseudo-dodecahedron and BO6 octahedron (VA and VB, respectively) as well as the associated A-O and B-O bond lengths. The interatomic angles of B-O1-B and B-O2-B decrease from 145.2–145.8° at 4.2(1) GPa to 143.3–143.5° at 64.6(6) GPa. Quantitative calculations of octahedral tilting angles (Ф) show that Ф increases smoothly with pressure. We found a linear relationship between the polyhedral volume ratio and the Ф in the bridgmanite with different compositions: VA/VB = –0.049Φ + 5.549. Our results indicate an increased distortion of the Fe10-Al14-Bgm structure with pressure, which might be related to the distortion of A-site Fe2+. The local environmental changes of A-site Fe2+ in bridgmanite could explain previous results on the hyperfine parameters, abnormal lattice thermal conductivity, mean force constant of iron bonds and other physical properties, which in turn provide insights into our understanding on the geophysics and geochemistry of the planet.
Human pyruvate dehydrogenase (E1) is a component enzyme of the pyruvate dehydrogenase complex. The enzyme catalyzes the decarboxylation of pyruvate followed by a reductive acetylation of lipoyl groups of the dihydrolipoamide acetyltransferase component of the pyruvate dehydrogenase complex. El is an alpha(sub 2)Beta(sub 2) tetrameric assembly of an approximate molecular mass of 154 kDa. The crystals of this recombinant enzyme have been grown from polyethylene glycol 3350 using vapor diffusion method at 295K. The crystals are characterized as orthorhombic, space group P2(sub 1)2(sub 1)2(sub 1), with cell parameters of a = 64.2, b = 126.9 and c = 190.2 A. Crystals diffracted to a minimum d-spacing of 2.5 A. The asymmetric unit contains one alpha(sub 2)Beta(sub 2) tetrameric El assembly, and self-rotation function analysis showed a pseudo-twofold symmetry relating the two monomers.
A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated projections, starting with no initial phase information. The practicality of the method is demonstrated by simulation using known structures that exist in multiple crystal forms, assuming some information on the molecular envelope and positional relationships between the molecules in the different unit cells. With incorporation of new or existing methods for determination of these parameters, the approach has potential as a method for ab initio phasing.
Four new d 0 transition metal tellurites, namely InVTeO 6 (1), β-InVTe 2 O 8 (2), FeVTe 2 O 8 (3), and Fe 2 MoTe 2 O 10 (4), were synthesized under hydrothermal conditions, and their crystal structures were determined using single-crystal X-ray diffraction. Compound 1 crystallizes in the noncentrosymmetric space group P2 1 2 1 2 1 (No. 19), with unit cell parameters of a = 5.0759(2) Å, b = 8.5030(3) Å, c = 11.6376(5) Å, V = 502.28(3) Å 3 , and Z = 4, while the other three compounds crystallize in centrosymmetric structures, with space group Cmca and unit cell parameters of a = 7.0633(7) Å, b = 8.962(1) Å, c = 20.162(2) Å, V = 1276.3(2) Å 3 , and Z = 8 for compound 2, space group P2 1 /n and unit cell parameters of a = 7.8901(2) Å, b = 4.9617(1) Å, c = 16.4290(3) Å, β = 93.6198(8)°, V = 641.88(2) Å 3 , and Z = 4 for compound 3, and space group Pnma and unit cell parameters of a = 8.7878(2) Å, b = 6.1327(2) Å, c = 15.2423(4) Å, V = 821.45(4) Å 3 , and Z = 4 for compound 4. Compound 3 adopts a two-dimensional (2D) sheet structure composed of FeO 6 octahedra, VO 4 tetrahedra, and TeO 4 polyhedra. The other three compounds exhibit three-dimensional (3D) framework structures: Compound 1 is built from InO 6 octahedra, VO 4 tetrahedra, TeO 4 polyhedra; Compound 2 consists of InO 6 octahedra, VO 5 square pyramids, and TeO 3 polyhedra; and Compound 4 is composed of FeO 6 octahedra, MoO 6 octahedra, and TeO 3 polyhedra. The band structures, density of states, and electron localization functions of all four compounds were calculated. The vibrational spectra were examined for compounds 1, 2, and 4. Furthermore, powder X-ray diffraction, element analysis, and thermogravimetric analysis were conducted for compound 4.