bluuebunny/crossref_metadata_2025 huggingface dataset:
Intergrowth polytypoids as modulated structures: a superspace description of the Sr
n
(Nb,Ti)
n
O3n + 2 compound series
Authors: Elcoro L. , Perez-Mato J. M. , Withers R. L.
Published: July 2002

A new, unified superspace approach to the structural characterization of the perovskite-related Sr
n
(Nb,Ti)
n
O3n + 2 compound series, strontium niobium/titanium oxide, is presented. To a first approximation, the structure of any member of this compound series can be described in terms of the stacking of (110)-bounded perovskite slabs, the number of atomic layers in a single perovskite slab varying systematically with composition. The various composition-dependent layer-stacking sequences can be interpreted in terms of the structural modulation of a common underlying average structure. The average interlayer separation distance is directly related to the average structure periodicity along the layer stacking direction, while an inherent modulation thereof is produced by the presence of different types of layers (particularly vacant layers) along this stacking direction. The fundamental atomic modulation is therefore occupational and can be described by means of crenel (step-like) functions which define occupational atomic domains in the superspace, similarly to what occurs for quasicrystals. While in a standard crystallographic approach, one must describe each structure (in particular the space group and cell parameters) separately for each composition, the proposed superspace model is essentially common to the whole compound series. The superspace symmetry group is unique, while the primary modulation wavevector and the width of some occupation domains vary linearly with composition. For each rational composition, the corresponding conventional three-dimensional space group can be derived from the common superspace group. The resultant possible three-dimensional space groups are in agreement with all the symmetries reported for members of the series. The symmetry-breaking phase transitions with temperature observed in many compounds can be explained in terms of a change in superspace group, again in common for the whole compound series. Inclusion of the incommensurate phases, present in many compounds of the series, lifts the analysis into a five-dimensional superspace. The various four-dimensional superspace groups reported for this incommensurate phase at different compositions are shown to be predictable from a proposed five-dimensional superspace group apparently common to the whole compound series. A comparison with the scarce number of refined structures in this system and the homologous (Nb,Ca)6Ti6O20 compound demonstrates the suitability of the proposed formalism.
(3 + 2)-Dimensional superspace approach to the structure of the stage-2 misfit layer compound (SbS)1.15(TiS2)2
Authors: Ren Y. , Meetsma A. , Wiegers G. A. , van Smaalen S.
Published: July 2002

The inorganic misfit layer compound (SbS)1.15(TiS2)2 was prepared by high-temperature reaction of the elements. It can be regarded as a stage-2 phase intercalation compound where double layers of SbS are inserted into the van der Waals gaps of TiS2 with stacking sequence ...[TiS2][SbS][TiS2][TiS2][SbS][TiS2].... The structure, determined by single crystal X-ray diffraction on the basis of the (3 + 2)-dimensional superspace group C{\bar 1}, is described by two interpenetrating, incommensurately modulated subsystems. The first subsystem comprises double sandwiches of TiS2 with 1T-TiS2 structure. The lattice parameters are a
11 = 3.404 (1), a
12 = 5.908 (3), a
13 = 17.068 (3) Å, α
1 = 86.28 (2), β
1 = 96.40 (2) and γ
1 = 90.00 (2)°. The second subsystem is built of intrinsically interface modulated double layers of SbS. Unit-cell dimensions of the basic structure are given by a
21 = 2.950 (1), a
22 = 5.932 (2), a
23 = 17.008 (2) Å, α
2 = 85.82 (1), β
2 = 85.30 (1), γ
2 = 84.11 (1)°. The interface modulation wavevector of SbS is given by q = 0.411 (2)a*21 + 0.822 (4)a*22. The two subsystems have the common (a*
v2, a*
v3) plane. Refinement on 3112 reflections with I > 2.5σ(I) converged to R = 0.088 (wR = 0.108). The structure consists of both occupational and displacive modulations for the atoms in the SbS subsystem. The SbS subsystem has the same structural features as found in the compound (SbS)1.15TiS2 [Ren, Meetsma, Petricek, van Smaalen & Wiegers (1995), Acta Cryst. B51, 275–287]. But stacking disorder of SbS is found corresponding to displacements of the layers along the a
21 axis; the final structure model involves a rigid shift of 0.63 (2) Å of 5.5 (4)% of SbS to both sides along a
21.
Structure of the polytypic β-form of P3N3(OCH2CF2CF2CH2O)F4
Authors: Wang Z. , Willett R. D. , Elias A. J. , Kirchmeier R. L. , Shreeve J. M.
Published: July 2002

Crystals of the β-form of the title compound, 1,1,3,3-tetrafluoro-5,5-(2,2,3,3-tetrafluorotetramethylenedioxy)cyclotri(phosphazene), are triclinic, P{\bar 1}, with lattice constants a = 12.392 (2), b = 16.569 (3), c = 19.257 (4) Å, α = 110.22 (3), β = 90.02 (3), γ = 97.10 (3)° and V = 3677.9 (12) Å3 with Z = 12, to yield P
calc = 2.010 Mg m−3 for Mr
= 371.0 and F(000) = 2184. The structural data was refined to R = 0.0548 and wR = 0.0567 for 5536 observed reflections [|F| ≥ 3σ(F)] with a goodness-of-fit of 1.61 and a maximum residual of 0.47 e Å−3. The six crystallographically independent molecules are all structurally equivalent, with approximately the same orientation for each molecule. The molecules are roughly arranged in layers lying parallel to the ac plane. Two types of these layers exist within the structure. Each layer exhibits approximate noncrystallographic symmetry elements. For layers at y ~ {{1}\over{6}} and {{5}\over{6}}, the appropriate layer-group symmetry notation is pc2a, while the layer at y ~ {{1}\over{2}} has idealized p21/c11 symmetry. The difference in the symmetries of the two types of layers arises from different sequencing of molecules with right- and left-handed chirality. Both layer groups require β to be equal to 90°, explaining its observed value. The structure can be described as a polytype structure, in which stacking faults occur every third layer. An ABAABA stacking pattern exists, where A corresponds to the layer at y = {{1}\over{6}} and {{5}\over{6}} while B corresponds to the layer at y = {{1}\over{2}}. In addition, successive layers are related by the following set of idealized translation vectors \eqalign{T_{A,B} & = T_{B,A} = ({1\over 2},{1\over 3},{1\over 3})\cr T_{A,A} & = (0,{1\over 3},{1\over 3}).}Superimposed upon these translation vectors is modulation of the chirality of the molecules.
Conformational Analysis of Macrocyclic Ether Ligands. II. 1,4,7,10,13-Pentaoxacyclopentadecane and 1,4,7,10,13-Pentathiacyclopentadecane
Authors: Raithby P. R. , Shields G. P. , Allen F. H.
Published: July 2002

Crystallographic results retrieved from the Cambridge Structural Database (CSD) have been used to perform a systematic conformational classification of free and metal-coordinated unsaturated 15-membered oxa and thia macrocycles using symmetry-modified Jarvis-Patrick cluster analysis. Relative molecular mechanics energies of the observed conformations are compared with the cluster populations. With oxa donors a uniangular and a [348] conformer predominate for larger metal ions; these lie above the donor atom plane with 1–6 additional ligands bound on the same side. With smaller cations an anangular conformer is adopted, the O atoms describing the equatorial plane of a pentagonal bipyramid. Other conformers occur as dictated by the coordination environment, particularly if not all donor atoms are metal-bound; in some cases the conformation is determined by a hydrogen-bonded network. In some thia examples the ligand binds to an axial/apical and four equatorial sites of the coordination polyhedron; in others containing AuI or AgI the metal is linearly or tetrahedrally coordinated with additional M—S interactions. With mixed donors, the hard/soft characteristics of the metal determine the coordination mode.
Use of X-ray Anomalous Dispersion: the Superstructure of PbZrO3
Authors: Soejima Y. , Yamasaki K. , Fischer K. F.
Published: July 2002

Intensity measurements of several superlattice reflections of lead zirconate, PbZrO3, have been made on single-crystal specimens as a function of incident X-ray energy around the Pb L
III and Zr K absorption edges. Anomalies in the squared structure factor ∣F(hkl)∣2 of superlattice reflections with l odd, and of those with l even, are observed at both the absorption edges. This indicates that both Pb and Zr atoms show an out-of-phase type of displacement, not only on the xy plane but also along the z axis in the orthorhombic cell. The results of the Zr displacement are in contradiction with the models in the literature. It is shown that the use of X-ray anomalous dispersion is effective to obtain information on the atomic displacement and to investigate the superstructure.
Structure of Two Disordered Molybdates, Li2MoIVO3 and Li4Mo3
IVO8, from Total Neutron Scattering
Authors: Hibble S. J. , Fawcett I. D. , Hannon A. C.
Published: July 2002

The structures of the disordered lithium molybdates Li2MoO3 and Li4Mo3O8 have been investigated using total neutron scattering from polycrystalline powders. Rietveld analysis of the Bragg scattering is used to determine the average structures. Shortcomings in this method of analysis are demonstrated by comparing the total correlation function, T(r), determined from total neutron scattering, with those calculated from the structures determined from Rietveld analysis. Much more satisfactory models for these materials are derived from the structurally related ordered material LiZn2Mo3O8, using information from Mo K-edge extended X-ray absorption fine-structure spectroscopy (EXAFS). These models include metal–metal-bonded Mo3O13 clusters [d(Mo—Mo) = 2.58 Å in Li2MoO3 and 2.56 Å in Li4Mo3O8] not present in the average structure determined from Rietveld analysis [d(Mo—Mo) = 2.88 Å in Li2MoO3]. In contrast to EXAFS studies neutron diffraction yields information on all the pair correlations in the material, not merely those involving molybdenum, and allows, for example, the location of lithium. Remaining discrepancies between our models and the experimental T(r)'s give an insight into the disorder in the two materials.
Formation of One-Dimensional Chains, Two-Dimensional Bilayers and a Three-Dimensional Diamondoid Architecture in Hydrogen-Bonded Adducts of 4,4'-Biphenol with 1,4-Diazabicyclo[2.2.2]octane and 1,2-Diaminoethane
Authors: Ferguson G. , Glidewell C. , Gregson R. M. , Meehan P. R. , Patterson I. L. J.
Published: July 2002

In 4,4′-biphenol–1,4-diazabicyclo[2.2.2]octane (1/1), C12H10O2.C6H12N2 (1), monoclinic, C2/c, a = 12.1510 (9), b = 6.3202 (4), c = 21.051 (2) Å, β = 98.875 (10)° with Z = 4, the biphenol units lie across twofold rotation axes and the diamine units are disordered across centres of inversion. The molecular components are linked by means of O—H...N hydrogen bonds into zigzag chains with graph set C^{2}_{2}(16) running parallel to the [201] direction; the chains are not coiled and there are no interactions between neighbouring chains. In 4,4′-biphenol–1,2-diaminoethane–methanol (2/1/1), (C12H10O2)2.C2H8N2.CH4O (2), triclinic, P1¯, a = 9.4592 (7), b = 10.6311 (10), c = 12.2085 (14) Å, α = 91.812 (9), β = 93.091 (6), γ = 90.652 (6)° with Z = 2, there are seven independent hydrogen bonds of O—H...O, O—H...N and N—H...O types and each oxygen and each nitrogen acts as a single donor and single acceptor of hydrogen bonds. The four independent components are linked by means of O—H...O and O—H...N hydrogen bonds into a linear aggregate, and further O—H...N and O—H...O hydrogen bonds generate chains in the [011] direction containing alternating biphenol and diamine units, and in the [021] direction containing methanol and pairs of biphenol molecules. These two types of chain intersect to form a continuous two-dimensional net, graph set R^{10}_{10}(62), with biphenol molecules at the nodes: pairs of these nets are linked into bilayers by N—H...O hydrogen bonds, but the nets are not interwoven. In 4,4′-biphenol–1,2-diaminoethane (1/1), C12H10O2.C2H8N2 (3), monoclinic, P21/a, a = 8.2121 (5), b = 5.3401 (3), c = 14.6014 (9) Å, β = 99.962 (7)° with Z = 2, each of the components lies across a centre of inversion. The O atoms act as single donors and double acceptors of hydrogen bonds and the N atoms as double donors and single acceptors, so that both oxygen and nitrogen are effectively four-coordinate; all the hydrogen bonds are of O—H...N or N—H...O type. Chains built from N—H...O and O—H...N hydrogen bonds run parallel to [100] and [010] and the intersection of these gives two-dimensional nets built from R^{6}_{6}(12) rings: these nets are linked by the —C6H4C6H4— and —CH2CH2— spacer units into a continuous three-dimensional diamondoid structure.
Structural Investigations of the Phase Transitions of Tetramethylammonium Sulfate
Authors: Malchus M. , Jansen M.
Published: July 2002

Tetramethylammonium sulfate, [N(CH3)4]2SO4, was prepared in high purity via ion exchange. Two reversible first-order phase transitions at 263 ± 3 and 462 ± 3 K have been established by differential thermal analysis and temperature-dependent X-ray powder diffraction. Crystal structure determinations at 223 and 293 K reveal completely ordered sulfate and tetramethylammonium tetrahedra for the low-temperature modification, while at room temperature half of the sulfate groups are orientationally disordered. The space groups are P42/nmc with a = 7.5355 (9), c = 10.9910 (14) Å and Z = 2 [wR(F
2) = 0.089 for 239 independent reflections] and P4/nbm with a = 10.8948 (9), c = 10.789 (2) Å and Z = 4 [wR(F
2) = 0.118 for 792 independent reflections], respectively. Powder patterns, as recorded at 473 K by the Guinier–Simon X-ray technique, show that the high-temperature modification is cubic face-centered with a = 11.026 (2) Å and is likely to contain only free-rotating tetrahedra. The common aristotype of all three modifications is the fluorite-type structure. An examination of group–subgroup relations is made.
Interaction of lysine with iodic acid
Authors: Petrosyan A. M. , Sukiasyan R. P. , Terzyan S. S. , Burbelo V. M.
Published: July 2002

A new compound in the Lys–HIO3–H2O system (where Lys = lysine), lysine–iodic acid (1/3), C6H14N2O2.3HIO3, has been discovered. Its crystals display nonlinear optical properties. They were investigated by X-ray analysis, IR spectroscopy and NQR methods. The parameters of the unit cell are a = 8.360 (2), b = 6.330 (1), c = 14.750 (3) Å, β = 92.86 (3)°, D

x
= 2.87 Mg m−3, space group P21, Z = 2. The three iodate groups in the structure have different roles. Interaction of lysine and iodic acid results in a compound containing a doubly protonated lysine cation and two counterions, IO^-_3 and I2O5OH−.
Cation distribution and crystal chemistry of Y3Al5−x
Ga
x
O12 (0 ≤ x ≤ 5) garnet solid solutions
Authors: Nakatsuka Akihiko , Yoshiasa Akira , Yamanaka Takamitsu
Published: July 2002

Five single crystals of Y3Al5−x
Ga
x
O12 (0 ≤ x ≤ 5) garnet solid solutions with the compositions x = 0.0, 1.0, 2.0, 3.0 and 4.0 were synthesized using a flux method. The compositional dependence of the lattice constants of the garnet solid solutions shows a large deviation from Vegard's law. Investigation of the cation distributions of these garnets using single-crystal X-ray diffraction shows that Ga3+, which is larger than Al3+, preferentially occupies the tetrahedral (four-coordinate) site rather than the octahedral (six-coordinate) site. On the basis of the results obtained from structure refinements, geometric analyses of the polyhedral distortions were carried out. The results imply that the cation–cation repulsive force across the polyhedral shared edges decreases with increasing substitution of Ga3+. Moreover, the proportion of covalent bonding in the cation–oxygen bonds was estimated from the bond strength; the results indicate that the covalency of the Ga—O bond is greater than that of the Al—O bond. The peculiar cation distributions observed in the Y3Al5−x
Ga
x
O12 garnet solid solutions are most probably caused by the strong covalency of the Ga—O bond and also simultaneously induced by the need to decrease the cation–cation repulsive force. Crystal data: cubic, Ia3¯d, Z = 8, Mo Kα, λ = 0.71069 Å; at x = 0.0 (triyttrium pentaaluminium dodecaoxide): a
0 = 12.0062 (5) Å, V = 1730.7 (2) Å3, D

x
= 4.56 Mg m−3, M

r
= 593.613, μ = 21.21 mm−1, F(000) = 2224, R = 0.029 for 294 reflections; at x = 1.0 (triyttrium tetraaluminium gallium dodecaoxide): a
0 = 12.0432 (7) Å, V = 1746.7 (3) Å3, D

x
= 4.84 Mg m−3, M

r
= 636.351, μ = 24.09 mm−1, F(000) = 2368, R = 0.022 for 124 reflections; at x = 2.0 (triyttrium trialuminium digallium dodecaoxide): a
0 = 12.0926 (9) Å, V = 1768.3 (4) Å3, D

x
= 5.10 Mg m−3, M

r
= 679.089, μ = 26.85 mm−1, F(000) = 2512, R = 0.018 for 144 reflections; at x = 3.0 (triyttrium dialuminium trigallium dodecaoxide): a
0 = 12.1552 (6) Å, V = 1795.9 (3) Å3, D

x
= 5.34 Mg m−3, M

r
= 721.827, μ = 29.43 mm−1, F(000) = 2656, R = 0.018 for 184 reflections; at x = 4.0 (triyttrium aluminium tetragallium dodecaoxide): a
0 = 12.2123 (8) Å, V = 1821.3 (4) Å3, D

x
= 5.58 Mg m−3, M

r
= 764.565, μ = 31.97 mm−1, F(000) = 2800, R = 0.014 for 159 reflections.
The geometry and structural properties of the 4,8,12-trioxa-4,8,12,12c-tetrahydrodibenzo[cd,mn]pyrene system in the cationic state. Structures of a planar organic cation with various monovalent and divalent anions
Authors: Krebs Frederik C. , Laursen Bo W. , Johannsen Ib , Faldt André , Bechgaard Klaus , Jacobsen Claus S. , Thorup Niels , Boubekeur Kamal
Published: July 2002

The geometry of the 4,8,12-trioxa-4,8,12,12c-tetrahydrodibenzo[cd,mn]pyrene system in the cationic state was established by X-ray structural resolution of the salts formed between the cation and various anions. The geometry was found to be planar for the 4,8,12-trioxa-4,8,12,12c-tetrahydrodibenzo[cd,mn]pyrenylium and 2,6,10-tri(tert-butyl)-4,8,12-trioxa-4,8,12,12c-tetrahydrodibenzo[cd,mn]pyrenylium cations with the monovalent anions I−, BF_4^-, PF_6^-, AsF_6^-, HNO3.NO_3^- and CF3SO_3^-, and the divalent anions S2O_6^{2-} and Mo6Cl_{14}^{2-}. The salts were found to crystallize in distinct space groups following a characteristic pattern. Mixed cation–anion stacking resulted in space groups with high symmetry: Pbca in three cases and R3¯c in one; a temperature study of the latter was made at ten different temperatures. The formation of dimers of anions and cations resulted in lower-symmetry space groups, mainly monoclinic (P21/n, P21/c and C2/c), but also P1¯.
Structural chemistry of vanadium oxides with open frameworks
Authors: Zavalij Peter Y. , Whittingham M. Stanley
Published: July 2002

The present work is dedicated to a crystal-chemical and topographical analysis of vanadium oxides with open structures. The review covers, apart from a few exceptions, only pure vanadium oxide structures with vanadium in oxidation states greater than +3. Purely tetrahedral frameworks are not discussed because of their traditional, well known crystal chemistry and only a few examples of cluster compounds are provided. Structural classification and notation of vanadium oxide frameworks are proposed based on the following scheme: polyhedra → chain → layer → three-dimensional framework. Thus, approximately 60 types of vanadium oxide frameworks are divided into five classes by type of coordination polyhedra present and into 14 subclasses by a more complex structural formation. Details are also given of the analysis of vanadium–oxygen coordination polyhedra and their metamorphosis: tetrahedron–trigonal bipyramid–square pyramid–octahedron, as well as the combinatorial deduction of possible structures for the most common framework types.
Symmetry classification of the layered perovskite-derived A

n

B

n

X
3n+2 structures
Authors: Levin Igor , Bendersky Leonid A.
Published: July 2002

The effects of combinations of octahedral tilts on the symmetries of layered A

n

B

n

X
3n+2 structures were considered. Two complementary approaches were used to deduce the symmetries. The space groups associated with different tilt systems were determined for structures with different layer thicknesses (n values) and for structures with different layer stacking arrangements. For the most symmetrical tilts about the orthorhombic axes of the A

n

B

n

X
3n+2 structure, maximal group/subgroup relations were established. Comparison of these results with experimental data available in the literature suggests that the symmetries of most observed A

n

B

n

X
3n+2 compounds are fully determined by the tilt systems adopted by rigid BX
6 octahedra. The most common tilt system observed at room temperature is a combination of an in-phase tilt about an orthorhombic axis parallel to the pseudo-fourfold axis of the octahedron with a tilt about an orthorhombic axis perpendicular to the layers.
Correlation of structural and physico-chemical parameters with the bioactivity of alkylated derivatives of indole-3-acetic acid, a phytohormone (auxin)
Authors: Nigović Biljana , Antolić Snježana , Kojić-Prodić Biserka , Kiralj Rudolf , Magnus Volker , Salopek-Sondi Branka
Published: July 2002

As part of molecular recognition studies on the phytohormone indole-3-acetic acid (IAA) a series of alkylated IAAs has been examined. Phenyl-ring substitution (alkyl = methyl and ethyl) at positions 4-, 6- or 7- as well as pyrrole substitution at the 2- site resulted in the six compounds which are analyzed: 2-Me-IAA, 4-Me-IAA, 6-Me-IAA, 7-Me-IAA, 4-Et-IAA and 6-Et-IAA. The structure–activity relationships investigated include those between the geometrical parameters of the molecular structures determined by X-ray analysis, the growth-promoting activities in the Avena coleoptile straight-growth bioassay and relative lipophilicities calculated from retention times on a reversed-phase HPLC column and from R

F
values in reversed-phase TLC. Lipophilicities are correlated with the moments of inertia, average polarizability, molecular mass, and the van der Waals radii of the ring substituents. The influence of substitution on the electronic properties of the indole ring and its geometry is discussed on the basis of the UV and 1H NMR spectra.
Structures and physical properties of ∊-FeSi-type and CsCl-type RuSi studied by first-principles pseudopotential calculations
Authors: Vočadlo Lidunka , Price Geoffrey D. , Wood I. G.
Published: July 2002

An investigation of the relative stability of the two known polymorphs of RuSi, having the ∊-FeSi and CsCl structures, has been made by first-principles pseudopotential calculations. The resulting cell volumes and fractional coordinates at P = 0 are in good agreement with experiment. Application of high pressure to the ∊-FeSi phase of RuSi is predicted to produce a structure having almost perfect sevenfold coordination. However, it appears that RuSi having the CsCl-type structure will be the thermodynamically most stable phase for pressures greater than 3.6 GPa. Fitting of the calculated internal energy versus volume to a fourth-order logarithmic equation of state led to values (at T = 0 K) for the bulk modulus, K
0, of 202 and 244 GPa for the ∊-FeSi and CsCl phases, respectively, in excellent agreement with experiment. Band-structure calculations for both phases are also presented.
Neutron diffraction study of the atomic and molecular motion in hexamethylenetetramine
Authors: Duckworth J. A. K. , Willis B. T. M. , Pawley G. S.
Published: July 2002

An accurate neutron diffraction study has been carried out on a single-crystal of hexamethylenetetramine and the measured Bragg intensities have been analysed for the effects of thermal motion. Four different models of the thermal motion have been used in a least-squares refinement of the data: (1) conventional model with ellipsoidal atomic probability density functions; (2) cumulant expansion model with the thermal motion of each atom represented by both second and third cumulant coefficients; (3) as model (1) but including the restriction imposed on the temperature factors by assuming rigid-body molecular motion; (4) as model (2) but including the rigid-body restriction. The best fit is given by model (2), which takes into account deviations from the ellipsoidal atomic probability density functions brought about by libration. Of the rigid-body models, refinement is better for (4) than for (3). Two parameters only, (u
2) and (ω
2) of paper I (Willis & Pawley, Acta Cryst. (1970), A26, 254) are needed to specify the atomic thermal motions for models (3) and (4), whereas nine parameters are required for model (1) and twenty for model (2). The lone-pair electrons of the nitrogen atom have been detected by combining, in a difference Fourier synthesis, the present data with the X-ray measurements of Becka & Cruickshank (Proc. Roy. Soc. A (1963), 273, 435).
A prediction of Bijvoet intensity differences in the noncentrosymmetric structures of selenium and tellurium
Authors: McIntyre G. J.
Published: July 2002

The presence of an antisymmetric component of the non-spherical atomic charge distribution results in a more general breakdown of Friedel's law in polyatomic noncentrosymmetric structures. That this is also true in the case of noncentrosymmetric structures of elements is demonstrated directly for the case of the trigonal structures of Se and Te.
Low-resolution phase extension using wavelet analysis
Authors: Main Peter , Wilson Julie
Published: July 2002

A method to extend low-resolution phases is presented which uses histogram matching not only of the electron density, but also of histograms obtained from the different levels of detail provided by the wavelet transform of the electron density. Statistical values for the wavelet coefficients can be predicted and depend only on the resolution and solvent content. Therefore, new details can be added to an electron-density map by matching the values of the wavelet coefficients to those predicted for an increased resolution. The positions of the new details are also guided by the diffraction pattern. In this way, the resolution can be increased gradually; on a number of trial structures of different size, solvent percentage and space group, it has been possible to extend the phasing from 10 Å to around 6–7 Å.
Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+
Authors: Britton K. Linda , Rogers H. Fiona , Asano Yasuhisa , Dairi Tohru , Kato Yasuo , Stillman Timothy J. , Rice David W.
Published: July 2002

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 Å resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 Å and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.
Carboxypeptidase A: Native, Zinc-Removed and Mercury-Replaced Forms
Authors: Greenblatt H. M. , Feinberg H. , Tucker P. A. , Shoham G.
Published: July 2002

The crystal structure of the zinc-containing exopeptidase bovine carboxypeptidase A (CPA) has been refined to high resolution, based on a data set collected from a single crystal, incorporating new sequence information based on cloning of the bovine gene. In addition, new refined structures are available for the zinc-removed form of the enzyme, apo-CPA, as well as the mercury-replaced form, Hg-CPA. The native structure reveals that the zinc-bound water molecule does not appear to be more loosely bound than the rest of the zinc ligands, at least when B factor values are considered. Nor is there any evidence for a secondary location of this water molecule. The apo-enzyme structure does not show any density in the place of the removed zinc ion. The only significant change appears to be a χ2 rotation of one zinc histidine ligand to form an ion-pair interaction with a glutamic acid side chain. The structure of Hg-CPA reveals a solvent tris molecule bound to the mercury cation, as well as an unidentified cation bound to Glu270. The location of this cation agrees with previous proposals for the binding site of inhibitory zinc. These observations may explain some of the differences in kinetics observed in metal-replaced CPA.
Crystallization of two hCG-specific monoclonal antibody fragments
Authors: Fotinou Constantina , Beauchamp Jeremy , Emsley Paul , Black Isobel , deHaan Annemarie , Bos Ebo , Isaacs Neil W.
Published: July 2002

The Fab fragments of two monoclonal antibodies (Fab3A2, Fab6A) raised against epitopes of human chorionic gonadotrophin (hCG) have been crystallized using the vapour-diffusion technique. The Fab3A2 antibody recognises an epitope on the C-terminal peptide of the β-subunit and the Fab6A a conformational epitope of hCG. Both Fab crystals grow as hexagonal rods from ammonium sulfate solutions. The Fab3A2 crystals belong to space group P3121 with a = b = 74.84, c = 198.2 Å and diffract to 1.33 Å at the ESRF. The Fab6A crystals are in the space group P3221 with a = b = 129.53, c = 74.40 Å and diffract to 2.7 Å at the Daresbury SRS. One Fab molecule per asymmetric unit is present in both crystals.
Structure of d(TGCGCA)2 and a Comparison to Other DNA Hexamers
Authors: Harper Anne , Brannigan James A. , Buck Martin , Hewitt Lorraine , Lewis Richard J. , Moore Madeleine H. , Schneider Bohdan
Published: July 2002

The X-ray crystal structure of d(TGCGCA)2 has been determined at 120 K to a resolution of 1.3 Å. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the `pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388–11402] but with significantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA)2 with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na+, Mg2+ and Co3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure.
Plasticity, Hydration and Accessibility in Ribonuclease A. The Structure of a New Crystal Form and its Low-Humidity Variant
Authors: Sadasivan C. , Nagendra H. G. , Vijayan M.
Published: July 2002

The structures of a new crystal form of ribonuclease A and its low-humidity variant, each containing two crystallographically independent molecules, have been determined and refined. A detailed comparison of these structures with those of the other known crystal forms of the enzyme, which have different packing arrangements and solvent composition, leads to a meaningful delineation of the rigid and flexible regions of the protein molecule and the nature of its plasticity. Many of the water molecules which are common to all the structures are involved in bridging different regions of the protein molecule, thus emphasizing the role of water in stabilizing the tertiary structure. The analysis of the structures shows that for a given N or O atom, the level of hydration increases with accessible surface area, but levels off at an area of about 10 Å2. Generally, the hydration level tends to drop when the area increases beyond about 20 Å2. This drop correlates with an increase in the displacement parameter. The analysis also suggests that the van der Waals radii and probe radius normally used in accessible surface area calculations are not appropriate for dealing with all situations.
Crystallization and preliminary crystallographic study of tropinone reductase II from Datura stramonium
Authors: Yamashita Atsuko , Nakajima Keiji , Kato Hiroaki , Hashimoto Takashi , Yamada Yasuyuki , Oda Jun'ichi
Published: July 2002

Tropinone reductase II is an NADPH-dependent oxidoreductase involved in a plant alkaloid metabolism. The enzyme from Datura stramonium has been crystallized using 2-methyl-2,4-pentanediol as a precipitant and a macro-seeding technique. The crystal belongs to space group P42212, with cell dimensions a = b = 62.8 Å and c = 128.4 Å. A data set to 2.6 Å resolution has been collected at a cryogenic temperature.
Crystallization and preliminary crystallographic analysis of the major horse allergen Equ c 1
Authors: Grégoire Christophe , Tavares Gisele A. , Lorenzo Hans K. , Dandeu Jean-Pierre , David Bernard , Alzari Pedro M.
Published: July 2002

The secreted protein Equ c 1 is the major component responsible for the induction of specific IgE antibodies in patients sensitized to horse allergens. Equ c 1 belongs to the lipocalin superfamily of hydrophobic ligand-binding proteins, which also includes other known allergens. Equilibrium sedimentation and gel-filtration studies demonstrate that both the glycosylated form of Equ c 1 purified from horse salivary glands and the non-glycosylated recombinant form expressed in bacteria exist predominantly as dimers in solution. As observed for other dimeric lipocalins, acidic pH and low protein concentration favour dimer dissociation. The recombinant form of Equ c 1 has been crystallized using ammonium sulfate as a precipitant. The crystals belong to the tetragonal space group P41212 with cell parameters a = b = 84.0, c = 56.1 Å, and contain a single molecule in the asymmetric unit. A complete data set from native crystals was collected at the synchrotron source in Hamburg to 2.9 Å resolution using a frozen crystal, and structure determination is in progress.
Crystallization of the haptoglobin–hemoglobin complex
Authors: Przybylska Maria , Sheppard Helen M. , Szilágyi Sándor
Published: July 2002

Two orthorhombic forms of crystals of the haptoglobin–hemoglobin complex were obtained using polyethylene glycol as precipitant. These crystals did not diffract well enough for data collection and work on the complex is no longer continued. However, the description of the crystallization conditions may be useful in future endeavors to obtain suitable crystals.
Crystallization and preliminary X-ray diffraction studies of mammalian purple acid phosphatase
Authors: Guddat Luke W. , McAlpine Alan S. , Hume David , de Jersey John , Hamilton Susan , Martin Jennifer L.
Published: July 2002

The oxidized form of purple acid phosphatase from pig allantoic fluid has been crystallized in the presence of phosphate using the hanging-drop technique. The crystals belong to the space group P212121 and have unit-cell parameters a = 66.8, b = 70.3, c = 78.7 Å. Diffraction data collected from a cryocooled crystal using a conventional X-ray source extend to 1.55 Å resolution. A knowledge of the three-dimensional structure of mammalian purple acid phosphatase will aid in understanding the substrate specificity of the enzyme and will be important in the rational design of inhibitors, with potential in the treatment of bone diseases.
Crystallization and preliminary crystallographic investigations of rhodanese from Azotobacter vinelandii
Authors: Bordo Domenico , Colnaghi Rita , Deriu Daniela , Carpen Aristodemo , Storici Paola , Pagani Silvia , Bolognesi Martino
Published: July 2002

The rhdA gene identified in Azotobacter vinelandii codes for a protein, RhdA, which displays rhodanese (thiosulfate–cyanide sulfurtransferase) activity. RhdA was overexpressed and purified to homogeneity. The protein crystallized in the orthorhombic space group P21212 with unit-cell parameters a = 44.4, b = 150.8, c = 53.8 Å; on a synchrotron source the diffraction patterns could be collected to a resolution limit of 1.8 Å. Evaluation of the crystal density indicates that the crystal lattice accommodates one molecule per asymmetric unit and that the solvent content is 59% of the total volume.
Crystallization and preliminary crystallographic study of HIP/PAP, a human C-lectin overexpressed in primary liver cancers
Authors: Abergel Chantal , Chenivesse Sabine , Stinnakre Marie-Georges , Guasco Sophie , Bréchot Christian , Claverie Jean-Michel , Devinoy Eve , Christa Laurence
Published: July 2002

Human HIP/PAP is an adhesion protein expressed in normal pancreatic and Paneth cells and overexpressed in hepatocellular carcinoma. HIP/PAP was crystallized using the Hampton Research Crystal Screen and SAmBA software to define the optimal crystallization protocol. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 30.73, b = 49.35, c = 92.15 Å and one molecule in the asymmetric unit. Flash-frozen crystals diffract to 1.78 Å resolution using synchrotron radiation. A molecular-replacement solution was obtained using the human Reg/lithostathine structure and the AMoRe software.
Expression, crystallization and preliminary X-ray analysis of the two amino-terminal Ig domains of the neural cell adhesion molecule (NCAM)
Authors: Kasper Christina , Rasmussen Hanne , Berezin Vladimir , Bock Elisabeth , Larsen Ingrid Kjøller
Published: July 2002

The two amino-terminal Ig domains of the rat neural cell adhesion molecule, NCAM, have been expressed in the yeast strain Pichia pastoris. The double domain consisting of 191 amino acids was overexpressed, purified and crystallized. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 47.1, b = 122.5, c = 72.9 Å and β = 98.3°. Assuming there are four double domains per asymmetric unit, Vm
is estimated to be 2.41 Å3 Da−1 and the solvent content to be 42.3%. A native data set has been collected from a single flash-frozen crystal to 1.85 Å resolution.
Crystallization within agarose gel in microgravity improves the quality of thaumatin crystals
Authors: Lorber B. , Sauter C. , Robert M. C. , Capelle B. , Giegé R.
Published: July 2002

To prevent crystals from moving in orbit and sedimenting upon their return to earth, the model protein thaumatin was crystallized in agarose gel in the Advanced Protein Crystallization Facility during the eight-day Space Shuttle mission STS-95 (November 1998). The quality of tetragonal crystals grown in microgravity was compared with that of controls prepared in parallel in the laboratory. On the basis of their diffraction properties, microgravity crystals were more ordered than crystals grown in gel on earth (the latter being, on average, better than reference crystals obtained in solution on earth). It is concluded that protein crystallization within a gel in microgravity may yield crystals of superior quality by combining the advantages of both environments. A possible explanation for the positive effect of microgravity on protein crystallization in gels involving the better quality of the nucleus is discussed.
Crystallization and preliminary diffraction studies of two quinoprotein alcohol dehydrogenases (ADHs): a soluble monomeric ADH from Pseudomonas putida HK5 (ADH-IIB) and a heterotrimeric membrane-bound ADH from Gluconobacter suboxydans (ADH-GS)
Authors: Chen Zhi-wei , Baruch Petra , Mathews F. Scott , Matsushita Kazunobu , Yamashita Tetsuo , Toyama Hirohide , Adachi Osao
Published: July 2002

Crystals of a soluble monomeric quinocytochrome alcohol dehydrogenase (ADH-IIB) and of a trimeric membrane-associated quinocytochrome alcohol dehydrogenase (ADH-GS) have been obtained. The ADH-IIB crystals are triclinic, with one monomer in the unit cell, and were obtained in the presence of PEG 8000, sodium citrate, HEPES buffer and 2-propanol. X-ray data were collected at 110 K to 1.9 Å resolution (R
merge = 6.4%) and the orientation of a methanol dehydrogenase search molecule (from Methylophilus methylotrophus W3A1) was obtained by molecular replacement. Preliminary refinement of this model (10.0–3.0 Å resolution, R = 0.37, R
free = 0.40) led to tentative identification of the two highest peaks in a native anomalous difference Fourier map as the Fe atom of the heme and a calcium ion interacting with the PQQ prosthetic group. The ADH-GS crystals are tetragonal, displaying six similar lattices, both primitive and centered, and were grown by the sitting-drop method after replacement of Triton X-100 by dodecylmaltoside or octaethylene glycol monododecyl ether in the presence of ammonium sulfate and sodium acetate buffer, with and without PEG 3500 and calcium ion. The best diffraction is obtained at 110 K where the resolution extends to about 4 Å in the a and b directions and about 3 Å in the c direction.
Crystallization of the N-terminal domain of human sex hormone-binding globulin, the major sex steroid carrier in blood
Authors: Grishkovskaya Irina , Sklenar Gisela , Avvakumov George V. , Dales David , Behlke Joachim , Hammond Geoffrey L. , Muller Yves A.
Published: July 2002

The amino-teminal laminin G-like domain of human sex hormone-binding globulin (SHBG), which contains the steroid-binding site and the dimerization domain, has been produced in Escherichia coli, purified to homogeneity and crystallized in complex with 5α-dihydrotestosterone (DHT) in two different crystal forms. Native data sets have been collected for tetragonal crystals (space group P4122 or P4322; unit-cell parameters a = 52.2, c = 148.4 Å) diffracting to 3.3 Å and trigonal crystals (R32; a = 104.0, c = 84.4 Å) diffracting to better than 1.6 Å. Since both crystal forms can only accommodate a single monomer in the asymmetric unit and share twofold rotational symmetry, it is proposed that the homodimer of this truncated form of SHBG, as observed in ultracentrifugation experiments, displays C
2 point-group symmetry.
X-ray diffraction of helices with arbitrary periodic ligand binding
Authors: Gu Jin , Yu Leepo C.
Published: July 2002

The classical formalism for studying diffraction from helical structures extended to include ligand binding is presented. The diffraction from such a binding pattern is the convolution of the Fourier transforms of the helix and the one-dimensional binding distribution. It is shown in the present analysis that it is not necessary to assume that the binding distribution is strictly periodic, as long as its Fourier transform can be determined. Analysis of the convolution gives a general expression for the diffracted intensities and the selection rule for the layer-lines. It shows two groups of layer-lines: one group is the familiar layer-line set from the original helix, while the other group shows reciprocal spacings shifted by 1/a from the original helix layer-lines, where a is the average repeat of the binding distribution. This group of layer-lines is contributed by the ligand only. By way of examples, calculated diffraction patterns from muscle actin filaments with bound myosin heads in three different binding patterns are presented. This approach provides a method for determining the ligand-binding distribution along helices by an analysis of their X-ray diffraction patterns.
Toxoplasma gondii adenosine kinase: expression, purification, characterization, crystallization and preliminary crystallographic analysis
Authors: Recacha Rosario , Talalaev Alexander , DeLucas Lawrence J. , Chattopadhyay Debasish
Published: July 2002

The obligate intracellular protozoan parasite Toxoplasma gondii depends on the purine-salvage pathway for its purine supply. Unlike its mammalian hosts, T. gondii salvages purine precursors predominantly via adenosine kinase, the enzyme that phosphorylates adenosine to adenosine monophosphate (AMP). The cDNA encoding T. gondii adenosine kinase was subcloned and expressed in Escherichia coli. The recombinant protein was active in an in vitro enzyme assay over a broad pH range. It required a divalent cation for activity. The enzyme was inactivated by the addition of 1 µM mercuric chloride. The inactivation could be reversed by a reducing agent. The active recombinant protein was crystallized using sodium sulfate as precipitant at pH 8.0. The crystals diffract to 1.8 Å and belong to the monoclinic space group P21, with unit-cell parameters a = 47.5, b = 68.9, c = 57.0 Å, β = 100.3°. The calculated Vm
based on one molecule per asymmetric unit is 2.38 Å3 Da−1.
The 2.0 Å structure of bovine interferon-γ; assessment of the structural differences between species
Authors: Randal Michael , Kossiakoff Anthony A.
Published: July 2002

The structure of bovine interferon-γ (IFN-γ) was determined by multiple isomorphous replacement at 2.0 Å resolution. Bovine IFN-γ crystallizes in two related crystal forms. Crystal form 1 diffracts to 2.9 Å resolution and is reproducible and stable to derivatization. Crystal form 2 diffracts to 2.0 Å resolution, but shows significant non-isomorphism from crystal to crystal. The previously determined structures of several different species of INF-γ were either at too low a resolution [human, 1hig; Ealick et al. (1991), Science, 252, 698–702] or were too inaccurate [bovine, 1rfb; Samudzi & Rubin (1993), Acta Cryst. D49(6), 505–512; rabbit, 2rig; Samudzi et al. (1991), J. Biol. Chem.
266(32), 21791–21797] for the structure to be solved by molecular replacement. The structure was solved in crystal form 1 using two derivatives produced by chemically modifying two free cysteine residues that were introduced by site-directed mutagenesis (Ser30Cys, Asn59Cys). After model building and refinement, the final R value was 21.8% (R
free = 30.9%) for all data in the resolution range 8.0–2.9 Å. The crystal form 1 structure was then used as a molecular-replacement model for crystal form 2 data collected from a flash-cooled crystal. Subsequent model building and refinement, using all data in the resolution range 15.0–2.0 Å, gave an R value of 19.7% and an R
free of 27.5%. Pairwise comparison of Cα positions of bovine IFN-γ (BOV) and the previously determined 1rfb and 2rig structures indicated some significant differences in the models (r.m.s.d. values for BOV to 1rfb, 4.3 Å; BOV to 2rig, 4.0 Å). An assessment of the quality of the structures was made using the 3D–1D algorithm [Eisenberg et al. (1992), Faraday Discuss.
93, 25–34]. The resulting statistical scoring indicated that BOV was consistent with expected criteria for a 2.0 Å structure, whereas both 1rfb and 2rig fell below acceptable criteria.
X-ray-excited optical luminescence of impurity atom in semiconductor
Authors: Ishii M. , Tanaka Y. , Komuro S. , Morikawa T. , Aoyagi Y. , Ishikawa T.
Published: July 2002

We observed the x-ray-excited optical luminescence (XEOL) of erbium-doped silicon (Si:Er) thin films to make a site-selective x-ray absorption fine structure (XAFS) measurement of an optically active Er atom. The undulator beam was used for the increment of the electron population in the excited state, and following XEOL at an infrared wavelength of 1.54 µm with minimum absorption loss in the host Si was detected. The edge-jump and XAFS oscillation were successfully obtained at the Er LIII-edge. This spectrum originated from inner-shell excitation and relaxation of only the optically active Er atom, indicating that site-selectivity at an atomic level was achieved.