bluuebunny/crossref_metadata_2025 huggingface dataset:
Three New Polymorphic Forms of Molybdenum Pentachloride
Authors: Beck J. , Wolf F.
Published: July 2002

Three new polymorphic modifications of molybdenum pentachloride could be obtained by solvothermal syntheses in CCl4 and SbCl5 as solvents. The structures have been solved by single-crystal X-ray diffraction. The already known structure of monoclinic \alpha-MoCl5 (C2/m) is not isomorphous with \alpha-NbCl5 and is better derived from the closest packing of Cl atoms of the Sm type with molybdenum occupying 1/5 of the octahedral holes. The triclinic structure of \beta-MoCl5 (P\overline 1) can be derived from hexagonal closest packing. The orthorhombic structure of \gamma-MoCl5 (Pnma) and the monoclinic structure of \delta-MoCl5 (P21/c) can both be derived from double-hexagonal closest packing. All four forms of MoCl5 have in common the discrete Mo2Cl10 moieties built from edge-sharing double octahedra with the metal atoms displaced from the octahedron centres away from each other. The differences between the modifications lie in the different stacking sequences of the close-packed Cl-atom layers and the different occupation of the octahedral interstices. This is reflected in the group–subgroup relationships of the space groups of the closest packings and the molybdenum pentachlorides. X-ray powder diffraction shows that sublimed MoCl5 is a mixture of all four modifications in variable amounts and probably a further unknown form.
Centrosymmetric or Noncentrosymmetric? Case Study, Generalization and Structural Redetermination of Sr5Nb5O17
Authors: Abrahams S. C. , Schmalle H. W. , Williams T. , Reller A. , Lichtenberg F. , Widmer D. , Bednorz J. G. , Spreiter R. , Bosshard Ch. , Günter P.
Published: July 2002

The possibility that the structure of the novel semiconducting perovskite-related material strontium niobium oxide, Sr5Nb5O17, refined by Schmalle et al. [Acta Cryst. (1995), C51, 1243–1246] in space group Pnn2, might instead belong to space group Pnnm has been investigated following an analysis of the atomic coordinates that indicated the latter space group to be more likely. All I
obs were carefully remeasured, first those within a hemisphere containing c
*, then all that lay within the full sphere of reflection. Refinement was undertaken, with each of two different sets of weights, in each space group. Each data set was used under three limiting intensity conditions: I
obs > 4σ(I
obs), I
obs > 2σ(I
obs) and finally with all reflections, but setting magnitudes with I
obs ≤ 0 equal to 0. Fourteen separate tests based only upon the X-ray diffraction data may be used to distinguish between Pnn2 and Pnnm. Nine tests favored the latter choice, four were indeterminate and one was not used. Seven further tests may be made on the basis of physical measurement; of these, three strongly indicated Pnnm, one was indeterminate and three could not be used. The evidence clearly suggests the space group is Pnnm. The use of all reflections, including those with negative magnitude set equal to zero, is essential to avoid ambiguity in the X-ray diffraction tests and achieve the highest reliability. Refinement with weights based on variances of Type A and Type B [Schwarzenbach et al. (1995). Acta Cryst. A51, 565–569] resulted in improved reliability compared with that obtained from a popular empirical weighting scheme. The revised structure differs in several respects from that published previously.
Structures and Photoreactivities of 2,4,6-Triisopropylbenzophenones
Authors: Fukushima S. , Ito Y. , Hosomi H. , Ohba S.
Published: July 2002

Crystal structures of 2,4,6-triisopropylbenzophenone (I) and its ten derivatives have been determined: (II) 2,4,6-triisopropyl-3′-methoxybenzophenone, (III) 3′-chloroformyl-2,4,6-triisopropylbenzophenone, (IV) methyl 3-(2,4,6-triisopropylbenzoyl)benzoate, (V) 2,4,6-triisopropyl-4′-methylbenzophenone, (VI) 4′-tert-butyl-2,4,6-triisopropylbenzophenone, (VII) 2,4,6-triisopropyl-4′-methoxybenzophenone, (VIII) 4-(2,4,6-triisopropylbenzoyl)benzoic acid, (IX) 4′-chloroformyl-2,4,6-triisopropylbenzophenone, (X) methyl 4-(2,4,6-triisopropylbenzoyl)benzoate and (XI) ethyl 4-(2,4,6-triisopropylbenzoyl)benzoate. The conformations of these molecules are essentially the same. The central carbonyl moiety is approximately coplanar with the 3′- or 4′-substituted phenyl group and perpendicular to the triisopropylphenyl ring. The photostability of (IX) and (X) in the solid state is attributed to the narrow reaction cavity of the triisopropylphenylcarbonyl moiety, i.e. the intramolecular movements of isopropyl groups in the triisopropylphenyl plane toward the carbonyl C atom are suppressed by intermolecular close contacts. One of the barriers for the photocyclization of (IX) and (X) is caused by a dimeric structure in crystals through the π–π interaction, which is the result of having a polar methoxycarbonyl or chloroformyl group at position 4′ of the phenyl ring.
Molecular co-crystals of 2-aminothiazole derivatives
Authors: Lynch Daniel E. , Nicholls Laura J. , Smith Graham , Byriel Karl A. , Kennard Colin H. L.
Published: July 2002

A series of molecular adducts of 2-aminothiazole derivatives – 2-aminothiazole, 2-amino-2-thiazoline and 2-aminobenzothiazole with the carboxylic-acid-substituted heterocyclics indole-2-carboxylic acid, N-methylpyrrole-2-carboxylic acid and thiophene-2-carboxylic acid – have been prepared and characterized using X-ray powder diffraction and in five cases by single-crystal X-ray diffraction methods. These five compounds are the adducts of 2-amino-2-thiazolium with indole-2-carboxylate [(C3H7N2S)+(C9H6NO2)−], and N-methylpyrrole-2-carboxylate [(C3H7N2S)+-(C6H6NO2)−], 2-aminobenzothiazolium with indole-2-carboxylate [(C7H7N2S)+(C9H6NO2)−], N-methylpyrrole-2-carboxylate [(C7H7N2S)+(C6H6NO2)−] and thiophene-2-carboxylate [(C7H7N2S)+(C5H3O2S)−]. All complexes involve proton transfer, as indicated by IR spectroscopy, while the five crystal structures display similar hydrogen-bonding patterns with the dominant interaction being an R^2_2(8) graph set dimer association between carboxylate groups and the amine/heterocyclic nitrogen sites. Futhermore, in each case a subsiduary interaction between an amino proton and a carboxylate oxygen completes a linear hydrogen-bonded chain. In addition to this, the indole-2-carboxylate molecules in the adduct structure with 2-amino-2-thiazolium form associated dimers which add to the hydrogen-bonding network.
Total neutron diffraction: a route to the correct local structure of disordered LaMo2O5 and its application to the model compound Zn2Mo3O8
Authors: Hibble Simon J. , Cooper Steven P. , Patat Saban , Hannon Alex. C.
Published: July 2002

Analysis of Bragg diffraction is the normal route to the structure of crystalline materials. Here we demonstrate the use of total neutron diffraction in determining the local structure in the disordered lanthanum molybdate LaMo2O5. An average structure with space-group symmetry P63/mmc accounts for the Bragg scattering and shows that the compound contains the rare Mo6O18 cluster and a unique type of Mo—Mo bonded sheet. However, this gives an incomplete picture of the structure, since it does not reveal how the sites with fractional occupancy are occupied at a local level. Two models describing possible local structures are constructed by removing symmetry elements present in the average structure. Total correlation functions, T(r), calculated from these structures, with space-group symmetry P63
mc and P3¯m1, are compared with the experimental T(r) to show the validity of these local structures. The close relationship between the T(r)'s of the component structures gives an insight into why disorder occurs in LaMo2O5. The calculated and experimental T(r)'s for a model compound, Zn2Mo3O8, are compared to show the agreement expected from an ordered crystalline material. Remaining discrepancies between our model and the experimental T(r) give an insight into the origin of additional disorder in LaMo2O5.
X-ray and neutron diffraction study of benzoylacetone in the temperature range 8–300 K: comparison with other cis-enol molecules
Authors: Herbstein Frank H. , Iversen Bo Brummerstedt , Kapon Moshe , Larsen Finn Krebs , Madsen Georg Kent Hellerup , Reisner George M.
Published: July 2002

The crystal structure of benzoylacetone (1-phenyl-1,3-butanedione, C10H10O2; P21/c, Z = 4) has been determined at 300, 160 (both Mo Kα X-ray diffraction, XRD), 20 (λ = 1.012 Å neutron diffraction, ND) and 8 K (Ag Kα XRD), to which should be added earlier structure determinations at 300 (Mo Kα XRD and ND, λ = 0.983 Å) and 143 K (Mo Kα XRD). Cell dimensions have been measured over the temperature range 8–300 K; a first- or second-order phase change does not occur within this range. The atomic displacement parameters have been analyzed using the thermal motion analysis program THMA11. The most marked change in the molecular structure is in the disposition of the methyl group, which has a librational amplitude of ∼20° at 20 K and is rotationally disordered at 300 K. The lengths of the two C—O bonds in the cis-enol ring do not differ significantly, nor do those of the two C—C bonds, nor do these lengths change between 8 and 300 K. An ND difference synthesis (20 K) shows a single enol hydrogen trough (rather than two half H atoms), approximately centered between the O atoms; analogous results were obtained by XRD (8 K). It is inferred that the enol hydrogen is in a broad, flat-bottomed single-minimum potential well between the O atoms, with a libration amplitude of ∼0.30 Å at 8 K. These results suggest that at 8 K the cis-enol ring in benzoylacetone has quasi-aromatic character, in agreement with the results of high-level ab initio calculations made for benzoylacetone [Schiøtt et al. (1998). J. Am. Chem. Soc.
120, 12117–12124]. Application [in a related paper by Madsen et al. (1998). J. Am. Chem. Soc.
120, 10040–10045] of multipolar analysis and topological methods to the charge density obtained from the combined lowest temperature X-ray and neutron data provides evidence for an intramolecular hydrogen bond with partly electrostatic and partly covalent character, and large p-delocalization in the cis-enol ring. This is in good agreement with what is expected from the observed bond lengths. Analysis of the total available (through the Cambridge Structural Database, CSD) population of cis-enol ring geometries confirms earlier reports of correlation between the degree of bond localization in the pairs of C—C and C—O bonds, but does not show the dependence of bond localization on d(O...O) that was reported earlier for a more restricted sample. It is suggested that the only reliable method of determining whether the enol hydrogen is found in a single or double potential well is by low-temperature X-ray or (preferably) neutron diffraction.
Synchrotron radiation study of yttria-stabilized zirconia, Zr0.758Y0.242O1.879
Authors: Ishizawa N. , Matsushima Y. , Hayashi M. , Ueki M.
Published: July 2002

The fluorite-related cubic structure of yttria-stabilized zirconia, Zr0.75
8Y0.24
2O1.87
9, has been studied by single-crystal X-ray diffraction using synchrotron radiation and by EXAFS. Two diffraction data sets obtained at X-ray energies of 512 and 10 eV below the Y K edge revealed that in the average structure Zr atoms are displaced from the origin of the space group Fm3¯m along 〈111〉 by 0.19 Å, while Y atoms reside at the origin. Approximately 48% of the O atoms occupy the ideal position in the fluorite-type structure, while 43% of O atoms are displaced from the ideal position along 〈001〉 by 0.31 Å. The remaining 9% of O atoms are presumably sited at interstitial positions. Local structures around Zr and Y are investigated by combining the results of single-crystal X-ray diffraction and EXAFS studies.
A comparative study of the crystal structures of tetrahalogenated hydroquinones and γ-hydroquinone
Authors: Thalladi Venkat R. , Weiss Hans-Christoph , Boese Roland , Nangia Ashwini , Desiraju Gautam R.
Published: July 2002

γ-Hydroquinone (1) and its tetrafluoro, tetrachloro and tetrabromo derivatives (2), (3) and (4) adopt crystal structures that have an almost invariant system of O—H...O hydrogen bonds. However, within this O—H...O framework, the four structures display variations that are characteristic of the C—H, C—F, C—Cl and C—Br groups. In the parent compound (1) aromatic rings are packed with a herringbone geometry, whilst in the halogenated derivatives (3) and (4), polarization-type halogen...halogen contacts are optimized. The fluoro derivative (2) is exceptional in that neither of the above possibilities is adopted, even though the O—H...O scaffolding does not per se prohibit either of them geometrically.
TEMPO radicals showing magnetic interactions. II. 4-(Benzylideneamino)-TEMPO and related compounds
Authors: Iwasaki Fujiko , Yoshikawa Joseph H. , Yamamoto Hajime , Takada Kiwamu , Kan-nari Eiji , Yasui Masanori , Ishida Takayuki , Nogami Takashi
Published: July 2002

X-ray crystal structure analyses were performed on 4-(Ar-methyleneamino)-TEMPO radicals at room temperature (TEMPO = 2,2,6,6-tetramethylpiperidyl-1-oxyl): Ar = Ph [4-(benzylideneamino)-2,2,6,6-tetramethylpiperidyl-1-oxyl], 4-MeS-Ph [2,2,6,6-tetramethyl-4-(4-methylthiobenzylideneamino)piperidyl-1-oxyl], 4-Me-Ph [4-(4-methylbenzylideneamino)-2,2,6,6-tetramethylpiperidyl-1-oxyl], 4-PhO-Ph [2,2,6,6-tetramethyl-4-(4-phenoxybenzylideneamino)piperidyl-1-oxyl], 4-MeSO_{2}-Ph [2,2,6,6-tetramethyl-4-(4-methylsulfonylbenzylideneamino)piperidyl-1-oxyl], 3-Py [2,2,6,6-tetramethyl-4-(3-pyridylmethylideneamino)piperidyl-1-oxyl] and 2-Naph [2,2,6,6-tetramethyl-4-(2-naphthylideneamino)piperidyl-1-oxyl]. Structures of Ph and 4-Me-Ph derivatives were also determined at 100 K. Some of these crystals have been revealed to show intermolecular ferromagnetic interactions at an extremely low temperature. Structural features of crystals of Ph, 4-MeS-Ph and 3-Py derivatives, which show ferromagnetic interactions, are very similar to each other. In these crystals, O atoms are arranged to form a sheet. The ferromagnetic interactions are considered to be transferred through O...H van der Waals' interactions of the \beta-H atoms of the neighboring TEMPO rings within the sheet. Between O...O sheets, the aryl groups are arranged in a herringbone manner. The crystal structure of the 4-Me-Ph derivative, which shows an antiferromagnetic interaction, is also pseudo-isostructural with those of Ph, 4-MeS-Ph and 3-Py derivatives, while the arrangement of the aryl groups is different. The packing mode of the crystals of the 4-MeSO_{2}-Ph derivative, of which the Weiss constant \theta is nearly zero, is very different from those of the other derivatives showing magnetic interactions. The fact that the crystal structure of the paramagnetic 4-MeSO_{2}-Ph derivative does not show the O...O sheet structure accompanying the O...\beta-H interactions indicates that the intermolecular ferromagnetic interactions through \beta-H atoms within the O...O sheet are important for these TEMPO radical crystals.
Interplay of hydrogen bonding and other molecular interactions in determining the crystal packing of a series of anti-β-ketoarylhydrazones
Authors: Bertolasi Valerio , Gilli Paola , Ferretti Valeria , Gilli Gastone , Vaughan Keith , Jollimore Jason V.
Published: July 2002

The crystal structures of six anti-β-ketoarylhydrazones are reported: (a1) (E)-2-(4-cyanophenylhydrazono)-3-oxobutanenitrile; (a2) (E)-2-(4-methylphenylhydrazono)-3-oxobutanenitrile; (a3) (E)-2-(4-acetylphenylhydrazono)-3-oxobutanenitrile; (a4) (E)-2-(2-methoxy-phenylhydrazono)-3-oxobutanenitrile; (a5) (E)-2-(2-acetylphenylhydrazono)-3-oxobutanenitrile; (a6) (E)-2-(2-nitrophenylhydrazono)-3-oxobutanenitrile. All compounds contain the π-conjugated heterodienic group HN—N=C—C=O and could form, at least in principle, chains of intermolecular N—H...O hydrogen bonds assisted by resonance (RAHB-inter). Compounds (a1) and (a2) form this kind of hydrogen bond though with rather long N...O distances of 2.948 (3) and 2.980 (2) Å, and compound (a6) undergoes the same interaction but even more weakened [N...O 3.150 (1) Å] by the intramolecular bifurcation of the hydrogen bond donated by the N—H group. The intrinsic weakness of the intermolecular RAHB makes possible the setting up of alternative packing arrangements that are controlled by an antiparallel dipole–dipole (DD) interaction between two C=O groups of the β-ketohydrazone moiety [compounds (a4) and (a5)]. The critical factors that cause the switching between the dif-ferent packings turn out to be the presence of hydrogen bonding accepting substituents on the phenyl and, most frequently, the intramolecular N—H...O bond with the O atom of the phenyl o-substituent. The crystal packing is widely determined by RAHB-inter (three cases) or DD (two cases) interactions. Only compound (a3) dis-plays a different packing arrangement, where the DD interaction is complemented by a non-resonant hydro-gen bond between a p-acetyl phenyl substituent and the hydrazone N—H group [N...O 2.907 (2) Å]. Crystal densities range from 1.24 to 1.44 Mg m−3 and are shown to increase with the number of intermolecular hydrogen bonds and other non-van der Waals interactions.
Channel- and layer-type anionic host structures in inclusion compounds of urea, tetraalkylammonium terephthalate/trimesate and water
Authors: Xue Feng , Mak Thomas C. W.
Published: July 2002

New crystalline adducts of tetraalkylammonium terephthalate/trimesate with urea and water molecules result from hydrogen-bond directed assembly of complementary acceptors and donors, and the anionic host lattices are described using the graph-set notation to identify distinct hydrogen-bonding motifs and patterns. Tetra-n-butylammonium terephthalate–urea–water (1/6/2), C46H104N14O12 (1), triclinic, space group P1¯, a = 8.390 (2), b = 9.894 (2), c = 18.908 (3) Å, α = 105.06 (2), β = 94.91 (1), γ = 93.82 (2)°, Z = 1, is composed of hydrogen-bonded terephthalate–urea layers, which are intersected by urea layers to generate a three-dimensional network containing large channels for accommodation of the cations. Tetraethylammonium terephthalate–urea–water (1/1/5), C25H58N4O10 (2), triclinic, P1¯, a = 9.432 (1), b = 12.601 (1), c = 14.804 (1) Å, α = 79.98 (1), β = 79.20 (1), γ = 84.18 (1)°, Z = 2, has cations sandwiched between hydrogen-bonded anionic layers. Tetraethylammonium trimesate–urea–water (1/2/7.5), C35H86N7O15.5 (3), triclinic, P1¯, a = 13.250 (1), b = 14.034 (1), c = 15.260 (1) Å, α = 72.46 (1), β = 78.32 (1), γ = 66.95 (1)°, Z = 2, manifests a layer-type structure analogous to that of (2). Tetra-n-propylammonium hydrogen trimesate–urea–water (1/2/5), C35H78N6O13 (4), orthorhombic, Pna21, a = 16.467 (3), b = 33.109 (6), c = 8.344 (1) Å, Z = 4, features hydrogen trimesate helices in a three-dimensional host architecture containing nanoscale channels each filled by a double column of cations.
Crystal chemistry of some synthetic 2-oxa-steroids: conformation, packing motifs and isostructurality
Authors: Anthony Addlagatta , Jaskólski Mariusz , Nangia Ashwini
Published: July 2002

The crystal structures of six synthetic 2-oxa-steroids (A-ring lactone steroids) have been determined by single-crystal X-ray diffraction. The conformation and hydrogen bonding in these oxa-steroids is compared with packing motifs in the natural steroids and the anabolic agent, Anavar®. O—H...O hydrogen bonding with lactone carbonyl O is the preferred arrangement in molecules with a C—OH group. The donor H atoms of A, B and D rings participate in C—H...O interactions with lactone carbonyl O and D-ring hydroxyl/ketone O acceptor atoms. The conformation of the lactone ring in these analogues is different from the natural androgens because replacement of the C2-methylene group by an O atom changes the geometry of the A ring. Two structurally related lactone steroids provide the first example of O—H...O/C—H...O interaction mimicry and furthermore the two components form a binary solid solution. The O—H...O and C—H...O hydrogen bonds in 2-oxa-steroid crystal structures are analysed and the observed preferences discussed in terms of geometric and chemical factors.
Short-range ordering of vacancies and Fermi surface of TiO
Authors: Castles J. R. , Cowley J. M. , Spargo A. E. C.
Published: July 2002

The structure of the disordered (high-temperature) phase of titanium monoxide has been studied by electron diffraction. Composition-dependent complex distributions of diffuse scattering are observed and interpreted in terms of short-range-ordered configurations of lattice vacancies. The proposition that the form of the diffuse scattering may correspond to ordering under the influence of long-range electronic energy terms and so show a direct relationship to the topology of the Fermi surface is examined.
Polarization factor for graphite X-ray monochromators
Authors: Hope H.
Published: July 2002

Comparison of Ni-filtered and graphite-monochromatized Cu Kα diffraction data indicates that the `ideally imperfect' monochromator polarization factor is not applicable.
An alternative description of the structures of Rh7Mg44 and Mg6Pd
Authors: Andersson S.
Published: July 2002

The structure types of Rh7Mg44 and Mg6Pd are described by means of packing octahedra and tetrahedra. The host structure common to the two types is a cubic intergrowth of two different building units. One unit has the Mg atoms arranged as the anions in Keggin's ion (PW12040
3-), and the other is an octahedrally capped block of the pyrochlore structure.
On the application of phase relationships to complex structures. XVI. A random approach to structure determination
Authors: Baggio R. , Woolfson M. M. , Declercq J. P. , Germain G.
Published: July 2002

With triple-phase relationships treated as linear equations it is possible to refine a set of phases from given initial values. Phases so obtained are better than those found by refining to self-consistency with the tangent formula. An investigation of the radius of convergence of the least-squares refinement process showed that a substantially correct solution may often be found even starting with random phases. Systems containing up to 300 phases have been investigated and the results and their implications are discussed. It is concluded that the random approach can, at the very least, be used to obtain 70--100 phases as a good starting point for phase development. There is also the possibility of obtaining a sufficient number of phases directly to define a reasonably complex structure, especially with a computer augmented by an array processor. A problem which can arise with linear equations, as with the tangent formula, is that the phases obtained do not adequately define the enantiomorph and give an E map with a pseudo centre of symmetry. Two methods of overcoming this problem are described.
Variance of X-ray intensities: effect of dispersion and higher symmetries
Authors: Wilson A. J. C.
Published: July 2002

The variance of X-ray intensities is W = Σ
2 + (k - 1)S
2 - Σ

i

Qi
|fi
|4, where Σ is the sum of the squares of the moduli of the atomic scattering factors fi
, S is the modulus of the sum of the squares of the atomic scattering factors, k is 1 for noncentrosymmetric crystals and 2 for centrosymmetric, Qi
is an integer depending on the space group and Wyckoff position, and the summation is over the atoms of the asymmetric unit. Values of Qi
for the general reflexions and general positions are tabulated for the line, plane and space groups; they tend to be moderately positive for the less symmetric space groups and large and negative for the more symmetric. Special reflexions and special positions are discussed briefly. Dispersion shows itself in the distinction between Σ and S and in the modulus signs in the final term.
X-ray scattering factors for O2− and N3−
Authors: Schwarz K. , Schulz H.
Published: July 2002

Form factors calculated from several theoretical models show that the Xα method is accurate to about 1%. With the latter scheme and the Watson-sphere model the atomic form factors for O2- and N3- are computed for varying sphere radii. To a first approximation this radial variation accounts for the different environments of such ions. Deviations of up to 25% in the scattering factors occur when compared with the results obtained from the wave functions of the corresponding neutral atom.
How to take advantage of non-crystallographic symmetry in molecular replacement: `locked' rotation and translation functions
Authors: Tong Liang
Published: July 2002

Many protein molecules form assemblies that obey point-group symmetry. These assemblies are often situated at general positions in the unit cell such that the point-group symmetry of the assembly becomes non-crystallographic symmetry (NCS) in the crystal. The presence of NCS places significant constraints on structure determination by the molecular-replacement method. The locked rotation and translation functions have been developed to take advantage of the presence of NCS in this structure determination, which generally requires four steps. (i) The locked self-rotation function is used to determine the orientation of the NCS assembly in the crystal, relative to a pre-defined `standard' orientation of this NCS point group. (ii) The locked cross-rotation function is used to determine the orientation of one monomer of the assembly in the standard orientation. This calculation requires only the structure of the monomer as the search model. (iii) The locked translation function is used to determine the position of this monomer relative to the center of the assembly. Information obtained from steps (ii) and (iii) will produce a model of the entire assembly centered at the origin of the coordinate system. (iv) An ordinary translation function is used to determine the center of the assembly in the crystal unit cell, using as the search model the structure of the entire assembly produced in step (iii). The locked rotation and translation functions simplify the structure-determination process in the presence of NCS. Instead of searching for each monomer separately, the locked calculations search for a single rotation or translation. Moreover, the locked functions reduce the noise level in the calculation, owing to the averaging over the NCS elements, and increase the signals as all monomers of the assembly are taken into account at the same time.
Crystallization of a complex between a novel C-terminal transmitter, HPt domain, of the anaerobic sensor kinase ArcB and the chemotaxis response regulator CheY
Authors: Kato Masato , Mizuno Takeshi , Hakoshima Toshio
Published: July 2002

The histidine-containing phosphotransfer (HPt) domain at the C-terminus of the anaerobic sensor kinase ArcB has been cocrystallized with the chemotaxis response regulator CheY by a hanging-drop vapor-diffusion method. Crystals belong to space group P212121 with unit-cell dimensions a = 55.32, b = 76.29 and c = 83.89 Å, with one molecule in the crystallographic asymmetric unit. The crystals diffract to 2.7 Å resolution. This is the first crystallization of a protein–protein complex formed by a transmitter domain of sensor kinase and a receiver domain of response regulator in the two-component signal-transduction system.
Water Molecules Hydrogen Bonding to Aromatic Acceptors of Amino Acids: the Structure of Tyr-Tyr-Phe Dihydrate and a Crystallographic Database Study on Peptides
Authors: Steiner Thomas , Schreurs Antoine M. M. , Kanters Jan A. , Kroon Jan
Published: July 2002

The crystal structure of Tyr-Tyr-Phe dihydrate contains a hydrogen bond formed between a water molecule and the Phe side chain. The geometry is centered with a distance of 3.26 Å between the water O atom and the aromatic centroid. In a database study on hydrated peptides, four related examples are found which exhibit a wide variability of hydrogen-bond geometries. The intermolecular surroundings of the water molecules are inspected, showing that they are typically involved in complex networks of conventional and non-conventional hydrogen bonds. Possible relevance for protein hydration is given.
Crystallization and preliminary crystallographic study of a component of the Escherichia coli Tol system: TolB
Authors: Abergel Chantal , Rigal Alain , Chenivesse Sabine , Lazdunski Claude , Claverie Jean-Michel , Bouveret Emmanuelle , Bénédetti Hélène
Published: July 2002

TolB from Escherichia coli is part of the Tol system used by the group A colicins to penetrate and kill cells. A TolB derivative tagged with six histidines was overexpressed, purified by chelation on a nickel affinity column and crystallized using the SAmBA software to define the optimal crystallization protocol. The crystals belong to the monoclinic system, space group P21 with unit-cell parameters a = 64.48, b = 41.06, c = 78.41 Å, β = 110.78°. Frozen crystals diffract to 1.9 Å resolution. Screening for heavy-atom derivatives both on the native TolB and various cysteine-substituted mutants is in progress. In addition, a selenomethionine-substituted protein is being produced in order to use the MAD method for structure determination.
Crystallization and preliminary X-ray crystallographic analysis of the helicase domain of hepatitis C virus NS3 protein
Authors: Kang Lin-Woo , Cho Hyun-Soo , Cha Sun-Shin , Chung Kyung Min , Back Sung Hoon , Jang Sung Key , Oh Byung-Ha
Published: July 2002

The NS3 protein of hepatitis C virus (HCV) is thought to be essential for viral replication. The N-terminal domain of the protein contains protease activity and the C-terminal domain contains nucleotide triphosphatase and RNA helicase activity. The RNA helicase domain of HCV NS3 protein was purified by using affinity-column chromatographic methods, and crystallized by using the microbatch crystallization method under oil at 277 K. The crystals belong to primitive trigonal space group P3121 or P3221 with cell dimensions of a = b = 93.3, c = 104.6 Å. The asymmetric unit contains one molecule of the helicase domain, with the crystal volume per protein mass (V

m
) of 2.50 Å3 Da−1 and solvent content of about 50.8% by volume. A native data set to 2.3 Å resolution was obtained from a frozen crystal indicating that the crystals are quite suitable for structure determination by multiple isomorphous replacement.
Expression, purification, crystallization and crystallographic characterization of dimeric and monomeric human neutrophil gelatinase associated lipocalin (NGAL)
Authors: Strong R. K. , Bratt T. , Cowland J. B. , Borregaard N. , Wiberg F. C. , Ewald A. J.
Published: July 2002

Crystals of the monomeric and dimeric forms of human neutrophil gelatinase associated lipocalin have been grown in hanging-drop vapor-diffusion trials using PEG as a precipitating agent with recombinant protein expressed in a baculovirus-based system. Crystals of monomeric NGAL belong to the cubic space group P432 with lattice constants a = b = c = 126.6 Å; crystals of dimeric NGAL belong to the tetragonal space group P41212 (or its enantiomorph P43212) with lattice constants a = b = 54.14 and c = 121.56 Å. Isomorphous crystals of the NGAL dimer can be grown in the presence of ligand: the tripeptide N-formyl-Met-Leu-Phe.
Crystallization and preliminary X-ray investigation of the complex of RNase Sa with wild-type barstar
Authors: Urbanikova Lubica , Sevcik Jozef
Published: July 2002

RNase Sa, an extracellular ribonuclease produced by Streptomyces aureofaciens, is inhibited by barstar, the natural protein inhibitor of barnase, the ribonuclease of Bacillus amyloliquefaciens. The complex of RNase Sa with wild-type barstar was crystallized by hanging-drop vapour diffusion. It was shown by sodium dodecyl sulfate polyacrylamide gel electrophoresis that RNase Sa and barstar are present in equimolar proportions in the crystals. The crystals are in the hexagonal space group P65 with unit cell dimensions a = b = 56.95, c = 135.8 Å. They diffract to 1.7 Å resolution at the DESY synchronton source. The asymmetric unit contains one molecule of the complex.
Transferability of Multipole Charge-Density Parameters: Application to Very High Resolution Oligopeptide and Protein Structures
Authors: Jelsch Christian , Pichon-Pesme Virginie , Lecomte Claude , Aubry André
Published: July 2002

Crystallography at sub-atomic resolution permits the observation and measurement of the non-spherical character of the electron density (parameterized as multipoles) and of the atomic charges. This fine description of the electron density can be extended to structures of lower resolution by applying the notion of transferability of the charge and multipole parameters. A database of such parameters has been built from charge-density analysis of several peptide crystals. The aim of this study is to assess for which X-ray structures the application of transferability is physically meaningful. The charge-density multipole parameters have been transferred and the X-ray structure of a 3_{10} helix octapeptide Ac-Aib_2-L-Lys(Bz)-Aib_2-L-Lys(Bz)-Aib_2-NHMe refined subsequently, for which diffraction data have been collected to a resolution of 0.82 Å at a cryogenic temperature of 100 K. The multipoles transfer resulted in a significant improvement of the crystallographic residual factors wR and wR free. The accumulation of electrons in the covalent bonds and oxygen lone pairs is clearly visible in the deformation electron-density maps at its expected value. The refinement of the charges for nine different atom types led to an additional improvement of the R factor and the refined charges are in good agreement with those of the AMBER molecular modelling dictionary. The use of scattering factors calculated from average results of charge-density work gives a negligible shift of the atomic coordinates in the octapeptide but induces a significant change in the temperature factors (\Delta B ≃ 0.4 Å2). Under the spherical atom approximation, the temperature factors are biased as they partly model the deformation electron density. The transfer of the multipoles thus improves the physical meaning of the thermal-displacement parameters. The contribution to the diffraction of the different components of the electron density has also been analyzed. This analysis indicates that the electron-density peaks are well defined in the dynamic deformation maps when the thermal motion of the atoms is moderate (B typically lower than 4 Å^2). In this case, a non-truncated Fourier synthesis of the deformation density requires that the diffraction data are available to a resolution better than 0.9 Å.
Protein Three-Dimensional Structural Databases: Domains, Structurally Aligned Homologues and Superfamilies
Authors: Sowdhamini R. , Burke David F. , Deane Charlotte , Huang Jing-fei , Mizuguchi Kenji , Nagarajaram Hampapathulu A. , Overington John P. , Srinivasan N. , Steward Robert E. , Blundell Tom L.
Published: July 2002

This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini & Blundell (1995), Protein Sci.
4, 506–520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali & Blundell (1990), J. Mol. Biol.
212, 403–428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.
Structure of recombinant human lactoferrin expressed in Aspergillus awamori
Authors: Sun Xiao-Lin , Baker Heather M. , Shewry Steven C. , Jameson Geoffrey B. , Baker Edward N.
Published: July 2002

Human lactoferrin (hLf) has considerable potential as a therapeutic agent. Overexpression of hLf in the fungus Aspergillus awamori has resulted in the availability of very large quantities of this protein. Here, the three-dimensional structure of the recombinant hLf has been determined by X-ray crystallography at a resolution of 2.2 Å. The final model, comprising 5339 protein atoms (residues 1–691, 294 solvent molecules, two Fe3+and two CO_3^{2-} ions), gives an R factor of 0.181 (free R = 0.274) after refinement against 32231 reflections in the resolution range 10–2.2 Å. Superposition of the recombinant hLf structure onto the native milk hLf structure shows a very high level of correspondence; the main-chain atoms for the entire polypeptide can be superimposed with an r.m.s. deviation of only 0.3 Å and there are no significant differences in side-chain conformations or in the iron-binding sites. Dynamic properties, as measured by B-value distributions or iron-release kinetics, also agree closely. This shows that the structure of the protein is not affected by the mode of expression, the use of strain-improvement procedures or the changes in glycosylation due to the fungal system.
Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A2
Authors: Sekar K. , Biswas R. , Li Y. , Tsai M.-D. , Sundaralingam M.
Published: July 2002

Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A2 have been determined at around 1.9 Å resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P212121. The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3121. The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.
Crystallization and preliminary X-ray analysis of the catalytic subunit of the ATP-dependent arsenite pump encoded by the Escherichia coli plasmid R773
Authors: Zhou Tongqing , Rosen Barry P. , Gatti Domenico L.
Published: July 2002

The arsenical resistance (ars) operon of the Escherichia coli plasmid R773 encodes a system for the active extrusion from cells of the toxic oxyanions arsenite (AsIIIO_{2}^{-}) and antimonite (SbIIIO_{2}^{-}) via an ATP-driven pump. The arsA and arsB genes of the operon encode the catalytic subunit (ATPase) and the membrane subunit of the pump, respectively. The arsC gene codes for a reductase that converts arsenate (AsVO_{4}^{3-}) to arsenite, thus extending bacterial resistance to the pentavalent state of arsenic. Crystals diffracting beyond 2.0 Å were obtained for the catalytic subunit of the pump (ArsA). These crystals belong to space group I222, with unit-cell parameters a ≃ 73, b ≃ 76, c ≃ 223 Å. A single molecule of ArsA, composed of two homologous halves, occupies the asymmetric unit of the I222 crystals with a predicted solvent content of 46%. Self-rotation function analysis suggests, however, that ArsA adopts a molecular packing corresponding to point group 422. One possible explanation of this result is that the two homologous halves of ArsA are related by a twofold axis of local symmetry and that the two halves of a `pseudo'-tetramer are related by a crystallographic twofold axis.
Automated MAD and MIR structure solution
Authors: Terwilliger Thomas C. , Berendzen Joel
Published: July 2002

Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.
Crystallization and preliminary X-ray analysis of the 6-phospho-α-glucosidase from Bacillus subtilis
Authors: Varrot Annabelle , Yamamoto Hiroki , Sekiguchi Junichi , Thompson John , Davies Gideon J.
Published: July 2002

6-Phospho-α-glucosidase (GlvA) is the protein involved in the dissimilation of α-glycosides accumulated via a phosphoenolpyruvate-dependent maltose phosphotransferase system (PEP-PTS) in Bacillus subtilis. The purified enzyme has been crystallized in a form suitable for X-ray diffraction analysis. Thin rod-like crystals have been grown by the hanging-drop method in the presence of manganese and NAD. They diffract beyond 2.2 Å using synchrotron radiation and belong to the space group I222 (or its enantiomorph) with unit-cell dimensions a = 83.26, b = 102.56, c = 145.31 Å and contain a single molecule of GlvA in the asymmetric unit.
Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 Å resolution
Authors: Ridder Ivo S. , Rozeboom Henriëtte J. , Dijkstra Bauke W.
Published: July 2002

Crystals of the 35 kDa protein haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 diffract to 1.15 Å resolution at cryogenic temperature using synchrotron radiation. Blocked anisotropic least-squares refinement with SHELXL gave a final conventional R factor of 10.51% for all reflections in the 15–1.15 Å resolution range. The estimated r.m.s. errors of the model are 0.026 and 0.038 Å for protein atoms and all atoms, respectively. The structure comprises all 310 amino acids, with 28 side chains and two peptide bonds in multiple conformations, two covalently linked Pb atoms, 601 water molecules, seven glycerol molecules, one sulfate ion and two chloride ions. Water molecules accounting for alternative solvent structure are modelled with a fixed occupancy of 0.5. The structure is described in detail and compared with previously reported dehalogenase structures refined at 1.9–2.3 Å resolution. An analysis of the protein's geometry and stereochemistry reveals eight mean values of bond lengths and angles which deviate significantly from the Engh & Huber parameters, a wide spread in the main-chain ω torsion angle around its ideal value of 180 (6)° and a role for C—H\cdotsO interactions in satisfying the hydrogen-bond acceptor capacity of main-chain carbonyl O atoms in the central β-sheet.
Crystallization and preliminary X-ray studies of metallothionein II from rabbit liver
Authors: An Yu , Li Genpei , Ru Binggen
Published: July 2002

Metallothionein II (Mw
= 6.8 kDa), induced by cadmium and purified from rabbit liver, has been crystallized in space group P6222 or P6422. The unit-cell parameters were a = b = 113.4, c = 219.1 Å, α = β = 90.0, γ = 120.0° when crystallized from sodium citrate buffer and a = b = 113.4, c = 219.6 Å, α = β = 90.0, γ = 120.0° when crystallized from Tris–HCl buffer. There are 12 molecules per asymmetric unit and the solvent content is about 57%.
Production, crystallization and preliminary X-ray analysis of the human integrin \alpha_1 I domain
Authors: Salminen Tiina A. , Nymalm Yvonne , Kankare Jussi , Käpylä Jarmo , Heino Jyrki , Johnson Mark S.
Published: July 2002

Integrin α1β1 is one of the main collagen receptors in many cell types. A fast large-scale production, purification and crystallization method for the integrin α1 I domain is reported here. The α1 I domain was crystallized using the vapour-diffusion method with a reservoir solution containing a mixture of PEG 4000, sodium acetate, glycerol and Tris–HCl buffer. The crystals beong to the C2 space group, with unit-cell parameters a = 74.5, b = 81.9, c = 37.3 Å, α = γ = 90.0, β = 90.8°. The crystals diffract to 2.0 Å and a 94.2% complete data set to 2.2 Å has been collected from a single crystal with an R
merge of 5.8%.
Crystal structure of epidoxorubicin–formaldehyde virtual crosslink of DNA and evidence for its formation in human breast-cancer cells
Authors: Podell Elaine R. , Harrington Daniel J. , Taatjes Dylan J. , Koch Tad H.
Published: July 2002

Epidoxorubicin and daunorubicin are proposed to be cytotoxic to tumor cells by catalyzing production of formaldehyde through redox cycling and using the formaldehyde for covalent attachment to DNA at G bases. The crystal structure of epidoxorubicin covalently bound to a d(CGCGCG) oligomer was determined to 1.6 Å resolution. The structure reveals slightly distorted B-form DNA bearing two molecules of epidoxorubicin symmetrically intercalated at the termini, with each covalently attached from its N3′ to N2 of a G base via a CH2 group from the formaldehyde. The structure is analogous to daunorubicin covalently bound to d(CGCGCG) determined previously, except for additional hydrogen bonding from the epimeric O4′ to O2 of a C base. The role of drug–DNA covalent bonding in cells was investigated with synthetic epidoxorubicin–formaldehyde conjugate (Epidoxoform) and synthetic daunorubicin–formaldehyde conjugate (Daunoform). Uptake and location of drug fluorophore in doxorubicin-resistant human breast-cancer cells (MCF-7/ADR cells) was observed by fluorescence microscopy and flow cytometry. The fluorophore of Daunoform appeared more rapidly in cells and was released more rapidly from cells than the fluorophore of Epidoxoform over a 3 h exposure period. The fluorophore appeared predominantly in the nucleus of cells treated with both conjugates. The difference in uptake is explained in terms of the slower rate of hydrolysis of Epidoxoform to the species reactive with DNA and a proposed slower release from DNA based upon the crystal structures.
Crystallization of recombinant Leishmania major pteridine reductase 1 (PTR1)
Authors: Gourley David G. , Luba James , Hardy Larry W. , Beverley Stephen M. , Hunter William N.
Published: July 2002

The enzyme pteridine reductase (PTR1) has recently been discovered in the protozoan parasite Leishmania and validated as a target for therapeutic intervention. PTR1 is responsible for the salvage of pteridines and also contributes to antifolate drug resistance. Structural analysis, in combination with ongoing biochemical characterization will assist the elucidation of the structure–activity relationships of this important enzyme and support a structure-based approach to discover novel inhibitors. Recombinant L. major PTR1 has been purified from an Escherichia coli expression system and used in crystallization experiments. Orthorhombic crystals have been obtained and data to 2.8 Å has been measured. The space group is P21212 or P212121 with unit-cell dimensions of a = 103.9, b = 134.7, c = 96.2 Å. One homotetramer, of molecular mass approximately 120 kDa, probably constitutes the asymmetric unit and gives a Matthews coefficient, Vm
, of 2.8 Å3 Da−1 and 56% solvent volume. Self-rotation function calculations show a single well defined non-crystallographic twofold axis with features that might represent additional elements of non-crystallographic symmetry. The detail of exactly what constitutes the asymmetric unit will be resolved by structure determination.