bluuebunny/crossref_metadata_2025 huggingface dataset:
A database study of the bonding and conformation of bis-sulfonylamide/-imide moieties
Authors: Bombicz P. , Czugler M. , Kálmán A. , Kapovits I.
Published: July 2002

The bonding and conformational characteristics of bissulfonylamides and analogous imides are compared. Structures (44 altogether) containing R—SO2—NQ—SO2—R′ units were retrieved from the Cambridge Structural Database. They are either neutral (Q-H, alkyl or aryl groups, hereto atoms such as O and S) or charged (Q = e−) and bearing the functions R, R′ = Me, Et or Ph, respectively. The principal conformations of the —SO2—NQ—SO2— bridge (open versus folded) are represented by sodium dibenzenesulfonamide (BSULFA) and dibenzenesulfonimide (NABSUF). In addition to the compounds possessing Q = alkyl or aryl functions, complexes with N-metal bonds could clearly be distinguished. The dominant forms of SVI—X (X = O, N C) bonds are characterized and correlated with the bond angles formed around the S atoms. The marked difference between the archetypes of the S—N bonds (i.e. nitrogen charged or neutral) indicated that the interdependence of the S—X bonds, i.e. the size and the shape of the SVI[O,O′,N,C] tetrahedra, are principally governed by the environment of the N atoms. The conformation symmetry and dissymmetry of the charged and neutral —SO2—NQ—SO2— moieties are described in terms of the internal rotations about the bonds in the R—S—N—S—R′ fragment.
Conformational Isomerism of the Host as a Factor in Molecular Recognition in Host–Guest Inclusion Complexes: Example of Tris(5-acetyl-3-thienyl)methane
Authors: Herbstein F. H.
Published: July 2002

The tripod molecule tris(5-acetyl-3-thienyl)methane (TATM) is a flexile molecule, i.e. one that can occur in many conformationally isomeric states (conformers), which forms host–guest inclusion complexes with a large variety of guests (solvents). Some 40-odd different types of guest have been reported to form inclusion complexes. Five different types of crystal structure (all racemic), with nine different guests, have been reported in the literature and structural information is available for 17 crystallographically independent TATM molecules; most of the guests are disordered. Our analysis of this (substantial but, nevertheless, incomplete) database shows that each group of crystallographically isomorphous structures contains a particular TATM conformer with characteristic torsion angles about the bonds between methane carbon and the three thienyl rings (τ1, τ2 and τ3); the range of torsion angles in a particular structural group does not exceed 10°. Conformers are in addition distinguished via the stereochemistry of the acetyl group; there are approximately equal numbers of examples with carbonyl oxygen syn or anti to ring sulfur, intermediate conformations not being found. So far three different types of conformer have been encountered for the TATM molecule considered as an entity. A necessary condition for the occurrence of a particular conformer type is that the torsion angles τ1, τ2 and τ3 are such that ring H atoms should not approach more closely than (say) 2.4 Å, but this is not sufficient as considerably larger distances are found in some conformer types. Crystallization of the inclusion complex from a particular solvent can be envisaged to occur as follows. The TATM solution will contain a Boltzmann distribution of host conformers, the distribution depending on temperature but not on the nature of the solvent. Under suitable temperature and solubility conditions, the solvent will crystallize together with the appropriate conformer to form the inclusion complex-nuclei formed at this recognition stage, then grow into crystallites of the inclusion complex. The perturbed Boltzmann distribution (depleted in appropriate conformer) will continuously revert to its equilibrium form by conversion of the non-appropriate into the appropriate conformer as the crystallization proceeds.
X-ray Studies on Crystalline Complexes Involving Amino Acids and Peptides. XXXIII. Crystal Structures of L- and DL-Arginine Complexed with Oxalic Acid and a Comparative Study of Amino Acid–Oxalic Acid Complexes
Authors: Chandra N. R. , Prabu M. M. , Venkatraman J. , Suresh S. , Vijayan M.
Published: July 2002

The DL- and L-arginine complexes of oxalic acid are made up of zwitterionic positively charged amino acid molecules and semi-oxalate ions. The dissimilar molecules aggregate into separate alternating layers in the former. The basic unit in the arginine layer is a centrosymmetric dimer, while the semi-oxalate ions form hydrogen-bonded strings in their layer. In the L-arginine complex each semi-oxalate ion is surrounded by arginine molecules and the complex can be described as an inclusion compound. The oxalic acid complexes of basic amino acids exhibit a variety of ionization states and stoichiometry. They illustrate the effect of aggregation and chirality on ionization state and stoichiometry, and that of molecular properties on aggregation. The semi-oxalate/oxalate ions tend to be planar, but large departures from planarity are possible. The amino acid aggregation in the different oxalic acid complexes do not resemble one another significantly, but the aggregation of a particular amino acid in its oxalic acid complex tends to have similarities with its aggregation in other structures. Also, semi-oxalate ions aggregate into similar strings in four of the six oxalic acid complexes. Thus, the intrinsic aggregation propensities of individual molecules tend to be retained in the complexes.
Pseudoacids. II. 2-Acylbenzoic Acid Derivatives
Authors: Valente E. J. , Martin S. B. , Sullivan L. D.
Published: July 2002

Structures of derivatives of cyclic o-acylbenzoic acids, including the chloride, endo- and exocyclic amides, esters and anhydrides, are examined. 3-Chloro-1(3H)-isobenzofuranone (1), orthorhombic, Pbca, a = 11.616 (5), b = 8.120 (3), c = 15.640 (9) Å; 3-methoxy-3-phenyl-1(3H)-isobenzofuranone (3), orthorhombic, P212121, a = 6.923 (2), b = 8.291 (4), c = 21.551 (8) Å; 3-hydroxy-3-phenyl-N-propyl-1(3H)-isoindolone (4), orthorhombic, P212121, a = 8.662 (4), b = 9.551 (7), c = 17.649 (14) Å; 3-(N-morpholino)-1(3H)-isobenzofuranone (5), triclinic, P1¯, a = 6.172 (4), b = 11.163 (7), c = 17.33 (2) Å, α = 105.91 (6), β = 99.85 (6), γ = 97.57 (5)°; 3-(2′-benzoylbenzoyloxy)-3-phenyl-1(3H)-isobenzofuranone (7), triclinic, P1¯, a = 9.694 (3), b = 10.505 (4), c = 11.163 (4) Å, α = 80.58 (3), β = 80.41 (3), γ = 76.49 (3)°; bis[1(3H)-isobenzofuranone-3-yl]ether (8), monoclinic, I2/a, a = 15.31 (2), b = 6.111 (12), c = 28.30 (5) Å, β = 101.61 (12)°. An open oxoacid tertiary amide is also described: N-morpholino 2′-benzoylbenzamide (6): monoclinic, P21/c, a = 6.844 (4), b = 15.696 (8), c = 14.154 (7) Å, β = 99.43 (4)°. Pseudoacid derivatives form planar isobenzofuran and isoindole rings, and the former aldehyde/ketone carbon–heteroatom endocyclic and exocyclic bond distances show bond length variations which correlate with the relative basicities of the attached groups. Structures of both endocyclic and exocyclic nitrogen pseudoamides are reported as well as examples of the normal–pseudoanhydride and the dipseudoanhydride.
Crystal Engineering Using Tris-phenols. Cross-Linked, Pairwise-Interwoven Two-Dimensional Nets in the 2:1 Adduct of 1,1,1-Tris(4-hydroxyphenyl)ethane with 1,2-Diaminoethane
Authors: Ferguson G. , Glidewell C. , Gregson R. M. , Meehan P. R.
Published: July 2002

In 1,1,1-tris(4-hydroxyphenyl)ethane–1,2-diaminoethane (2/1), [CH3C(C6H4OH)3]2.H2NCH2CH2NH2 (1), triclinic, P1¯, with Z = 2, a = 10.9430 (12), b = 11.1075 (12), c = 15.249 (2) Å, α = 98.672 (15), β = 96.312 (10), γ = 98.377 (13)°, the tris-phenol units form continuous two-dimensional nets, built from pseudo-hexagonal R^4_4(38) rings, interwoven pairs of which are cross-linked by the 1,2-diaminoethane units. Each tris-phenol unit acts as a triple donor, forming two O—H...O and one O—H...N hydrogen bonds, and as a double acceptor in two O—H...O hydrogen bonds: the diamine unit, in which the CH2 groups are disordered over two sets of sites with site-occupation factors of 0.740 (5) and 0.260 (5), respectively, acts as a double acceptor only and the N—H bonds play no role in the hydrogen bonding. The O...O distances in the O—H...O hydrogen bonds are 2.642 (2), 2.690 (2), 2.810 (2) and 2.835 (2) Å, and the two independent O...N distances are both 2.665 (3) Å. Adjacent bilayers are connected into a continuous three-dimensional array by C—H...O hydrogen bonds, all having a C...O distance of 3.468 (4) Å.
Investigation of the Cs
x
Rb1−x
TiOAsO4 Series. II. The Problems of Interpretation of Residual Electron Densities in a Polar Space Group
Authors: Thomas P. A. , Womersley M. N.
Published: July 2002

The problems of refinements of structures in a polar space group, such as Pna21, are illustrated by the example of crystals in the Cs2x
Rb2−2x
Ti2O2As2O8, caesium rubidium titanyl arsenate, series, which are isostructural with the well known non-linear optical crystal KTiOPO4. It is shown in particular that errors in the data collection and/or refinement tend to contribute positive residual electron density in sites which are related by an inversion operation to the real Cs/Rb sites. This phenomenon is a consequence of the presence of two minima in least-squares space, representing here the possible coordinate sets x,y,z and x,y,−z, for a polar structure and is exacerbated in these structures by the presence of strong inversion psuedo-symmetry. It is shown that in the worst case, the positive residual electron density can be eliminated and an improved agreement to the observed data obtained by refinement of a partially micro-twinned disordered structure in which the Cs/Rb occupancy is split between the main sites and the inversion-related sites. It is argued that the true structure is micro-twinned, including partial occupancy of the additional sites.
Distribution and Topology of the Electron Density in an Aluminosilicate Compound from High-Resolution X-ray Diffraction Data: the Case of Scolecite
Authors: Kuntzinger S. , Ghermani N. E. , Dusausoy Y. , Lecomte C.
Published: July 2002

The experimental electron density distribution in scolecite, CaAl2Si3O10.3H2O, has been derived from single-crystal high-resolution Ag Kα X-ray diffraction data. A statistical method based on the prediction matrix has been used to discuss the estimation of the valence populations (P
val) in the kappa least-squares refinements. The densities on the Si—O—Si and Si—O—Al bridges have been characterized using the topology of the electron density through its Laplacian at the bond critical points. The Si—O and Al—O bond features are related to the atomic environment and to the Si—O—T geometries (T = Si, Al).
Experimental charge density and electrostatic potential in nicotinamide
Authors: Miwa Yoshihisa , Mizuno Takashi , Tsuchida Kazunori , Taga Tooru , Iwata Yutaka
Published: July 2002

The accurate crystal structure of nicotinamide, 3-pyridinecarboxamide, was determined from X-ray and neutron diffraction experiments: C6H6N2O, Mr
= 122.13, monoclinic, P21/c, Z = 4. The electron distribution at 150 K was determined by the maximum entropy method and the electrostatic potential in the crystal was calculated by Fourier convolution of the electron distribution. The electrostatic properties of the nicotinamide molecule depend on the molecular conformation. The asymmetric electrostatic potential field observed above and below the pyridine-ring plane is related to the rotation of the carboxamide group with respect to the pyridine plane. The positive potential peak at the C4 atom of the pyridine ring extends to the C=O-group side of the plane. The asymmetry of the potential on the C4 atom is consistent with the stereospecificity of hydride transfer in NAD+/NADH oxidoreduction.
Search for Pnma materials with high-temperature structural phase transitions
Authors: Igartua J. M. , Aroyo M. I. , Kroumova E. , Perez-Mato J. M.
Published: July 2002

A systematic search for structures having a high-temperature structural phase transition can be carried out through the identification in the structural databases of those structures that can be considered pseudosymmetric. Pseudosymmetry in a crystal structure indicates the possibility of a similar configuration of higher symmetry. If the distortion relating both structures is small enough, it can be expected that the crystal acquires the more symmetric configuration through a Landau-type phase transition at a higher temperature. Here, we present the results of such a search among inorganic structures with space group Pnma retrieved from the Inorganic Crystal Structure Database. Pseudosymmetry has indeed been detected in those compounds with a known (displacive) Landau-type phase transition at higher temperatures. This is measured by a parameter Δ, which measures the maximal atomic displacement relating the pseudosymmetry-transformed structure and the original one. In most of these compounds with a known phase transition, this parameter was smaller than 1.0 Å for at least one minimal supergroup of Pnma. The database contains 144 additional structures with pseudosymmetry features under the same quantitative limit. A comparison of the Δ distributions in both sets of compounds suggests a smaller Δ window (with 0.7 Å as maximal value) for selecting the materials having maximal probability of exhibiting a phase transition at higher temperatures. A set of 58 compounds fulfils this criterion.
Conformational behaviour of bridging diphenylphosphido ligands
Authors: Barker John J. , Orpen A. Guy
Published: July 2002

Data retrieved from the Cambridge Structural Database for crystal structures containing (μ-diphenylphosphido) metal complexes, [M
2{μ-PPh2}] (where M is a d-block element), have been analysed to evaluate the conformational behaviour of these species. The observed distribution of torsion angles about the P—C bonds has been compared with the potential energy surface (PES) for phenyl rotations in a representative species [(AuBr)2{μ-PPh2}]− computed using the universal force field. Good agreement was obtained between the low-energy (<8 kJ mol−1 above the global minimum) regions of the PES and the occupied regions of the two-dimensional P—Ph rotor conformation space. Phenyl ring rotations occur by coupled, geared disrotatory and uncoupled conrotatory motions of the phenyl groups in this and other classes of PPh2 rotors.
The crystal structure of Ca7Zr7Ta6O36 refined using synchrotron-radiation data
Authors: Schmid Siegbert , Thompson John G. , Withers Ray L. , Ling Christopher D. , Ishizawa Nobuo , Kishimoto Shunji
Published: July 2002

Single-crystal X-ray diffraction data [synchrotron radiation; λ = 1.2682 (4) Å] are used to solve and refine the crystal structure of heptacalcium hexatantalum heptazirconium hexatriacontaoxide, Ca7Zr7Ta6O36. The structure adopts space group Fddd with cell dimensions a = 36.394 (1), b = 7.3674 (5), c = 31.006 (2) Å. The structure was solved by direct methods. Refinement using 1299 unique reflections leads to final values of R = 0.031 and wR = 0.034. The refined metal-atom ordering scheme is far from fully ordered and reminiscent of the A/B metal-atom ordering characteristic of the pyrochlore structure type. Bond-valence sums are calculated to confirm the plausibility of the crystal chemistry of Ca7Zr7Ta6O36.
Phase-transition-induced twinning in the 1:1 adduct of hexamethylenetetramine and azelaic acid
Authors: Hostettler Marc , Birkedal Henrik , Gardon Manuel , Chapuis Gervais , Schwarzenbach Dieter , Bonin Michel
Published: July 2002

The title compound, C6H12N4\cdotC9H16O4, undergoes several thermotropic phase transitions. The crystalline structure is layered, with sheets of azelaic acid linked to sheets of hexamethylenetetramine by hydrogen bonds. In the room-temperature phase, the azelaic acid molecules are disordered. By lowering the temperature, this disorder partially disappears. The ordering is clearly observed in reciprocal space where on the rods of diffuse scattering, present in the room-temperature phase, a series of superstructure reflections emerges. This phase transition leads to twin-lattice quasi-symmetry (TLQS) twinning. The structure of this twinned phase is explored in this paper. There are two orientational domains linked by a mirror plane which relates disordered orientations of the acid molecules above the phase transition. A single domain has space group P2_1/c. The structure has been solved and refined on the complete set of data to R
1 = 0.0469. The chains remain partially disordered, showing two acid groups with unequal population: the major form corresponding to a carboxylic acid and the minor to a carboxylate. The ordering of the structure, when going through the phase transition, is interpreted in terms of stabilization by C—H...O hydrogen bonding. A least-squares estimator of the twinning volume ratio is developed that gives an expression for the twinning ratio in terms of the intensities of nonoverlapping reflections. The twinning ratio obtained in the structure refinement compares very well with that obtained from this estimator.
Structures des phases paraélectrique et ferroélectrique de Pb2KNb5O15
Authors: Sciau Philippe , Calvarin Gilbert , Ravez Jean
Published: July 2002

The paraelectric and the ferroelectric/ferroelastic structures of Pb2KNb5O15 have been refined by the Rietveld method from neutron and X-ray powder diffraction data. The paraelectric phase is tetragonal (space group P4/mbm) with lattice parameters a

t
= 12.646 (1) and c

t
= 3.9551 (2) Å at 790 K. The Pb- and K-atom distribution has been determined. It was established that the Pb atoms situated on the 15-coordinate sites are not on the special position (2mm) but are distributed over two disordered positions as in the tetragonal phase of Pb2KTa5O15. The ferroelectric/ferroelastic phase is orthorhombic. The space group of the average structure is Cm2m and the lattice parameters are a

o
= 17.779 (2), b

o
= 18.015 (2), c

o
= 3.9209 (4) Å at 294 K and a

o
= 17.756 (1), b

o
= 18.019 (1), c

o
= 3.9141 (2) Å at 81 K. It is isostructural with the average ferroelectric/ferroelastic structure of PbNb2O6. The orthorhombic distortion is of the same order but the Curie temperature is lowered by the substitution 2K+–Pb2+. The structures of PbNb2O6, PbTa2O6, Pb2KNb5O15 and Pb2KTa5O15 are compared. The ferroelectric polarization of the niobates is due to both the Pb off-site position and the Nb displacements, which induce a distortion of the oxygen lattice. In PbTa2O6, the oxygen-lattice distortion is very weak. The polarization seems to be due only to the Pb atom. In the tantalates the substitution 2K+–Pb2+ should weaken the correlations between the Pb atoms and consequently suppress the ferroelectric transition. Only a local polarization should take place; this might be the origin of the dielectric relaxation observed in this compound.
Packing similarities of three isosteric molecules: 4,5-dichlorophthalic anhydride, 4,5-dibromophthalic anhydride and 5,6-dichlorobenzfurazan 1-oxide, including three polymorphs of 5,6-dichlorobenzfurazan 1-oxide
Authors: Ojala Charles R. , Ojala William H. , Britton Doyle , Gougoutas J. Z.
Published: July 2002

4,5-Dichlorophthalic anhydride (CPA) lies on a twofold axis in space group C2/c; the molecules pack as stacks of two-dimensional sheets. Polymorph A of 5,6-dichlorobenzfurazan 1-oxide (CBF; systematic name 5,6-dichloro-2,1,3-benzoxadiazole 1-oxide) is isomorphous with CPA with disordered CBF molecules being pseudo-isosteric with the CPA molecule. Polymorph C of CBF has similar unit-cell dimensions but the arrangement of the molecules in the cell is different. 4,5-Dibromophthalic anhydride occurs in space group P1¯ in a structure derived from the CPA structure. The four structures all have similar two-dimensional sheets of molecules, but differ, in addition to the disorder of the CBF molecules, in the stacking of successive sheets. There are three polymorphs of 5,6-dichlorobenzfurazan 1-oxide. In all three the molecules are disordered about twofold or pseudo-twofold axes. In all three the molecules form chains involving similar Cl...O contacts along the direction of the twofold axis. In polymorphs A and C these chains form virtually identical two-dimensional sheets with inter-chain C—H...O, C—H...N and Cl...Cl contacts, but with different stacking arrangements between the sheets. In polymorph B the chains are associated in face-to-face pairs with the same face-to-face overlap as in A, at an average distance of 3.42 Å compared to an average distance of 3.38 Å in A (cf. Table 8); there are no two-dimensional sheets.
Anhydrous ammonioguanidinium(2+) and dihydrated bis[aminoguanidinium(1+)] hexafluorosilicates: new co-products of preparing ferroelectric ammonioguanidinium(2+) hexafluorozirconate. Erratum
Authors: Ross C. R. , Bauer M. R. , Nielson R. M. , Abrahams S. C.
Published: July 2002

An error in printing is reported. In the paper by Ross et al. [Acta Cryst. (1999), B55, 246–254] the length of a bond formed by H3 is given incorrectly in the sixth sentence of the first paragraph of §3.3 on page 251. The sentence should read `The out-of-plane displacement modifies the hydrogen-bonding pattern, allowing an approach of 2.21 (2) Å to F2, see Table 4; the resulting increase in structural stability supports this model.'
Structure, phase transitions and ionic conductivity of K3NdSi6O15·xH2O. II. Structure of β-K3NdSi6O15
Authors: Haile S. M. , Wuensch B. J.
Published: July 2002

Hydrothermally grown crystals of β-K3NdSi6O15, potassium neodymium silicate, have been studied by single-crystal X-ray methods. Under appropriate conditions, the compound crystallizes in space group Bb21
m and has lattice constants a = 14.370 (2), b = 15.518 (2) and c = 14.265 (2) Å. There are 30 atom sites in the asymmetric unit of the basic structure. With eight formula units per unit cell, the calculated density is 2.798 Mg m−3. Refinement was carried out to a residual, wR(F
2), of 0.1177 [R(F) = 0.0416] using anisotropic temperature factors for all atoms. The structure is based on (Si2O5
2−)∞ layers, connected by Nd polyhedra to form a three-dimensional framework. Potassium ion sites, some of which are only partially occupied, are located within channels that run between the silicate layers. The silica–neodymia framework of β-K3NdSi6O15, in particular the linkages formed between the silicate layers and Nd polyhedra, bears some similarities to that of the essentially isocompositional phase α-K3NdSi6O15·2H2O. In both, the silicate layers are corrugated so as to accommodate a simple cubic array of NdO6 octahedra with lattice constant ∼ 7.5 Å. Furthermore, the Si2O5 layers in β-K3NdSi6O15 are topologically identical to those of the mineral sazhinite, Na2HCeSi6O15. Although β-K3NdSi6O15 and sazhinite are not isostructural, the structures of each can be described as slight distortions of a high-symmetry parent structure with space group Pbmm.
Is there an N3− ion in the crystal structure of the ionic conductor lithium nitride (Li3N)?
Authors: Schulz H. , Schwarz K.
Published: July 2002

The structure parameters of Li3N in the temperature range -120 to 20°C were refined both for neutral atoms (Li0 and N0) and for ions (Li+ and N3-). For N3- new scattering curves were used which were calculated by applying stabilizing Watson-sphere potentials for different radii. All structure parameters depend critically on the scattering curves used. However, only on the assumption of ions, and only for N3- scattering curves corresponding to a small range of Watson radii, were physically meaningful structure parameters and R values down to 0.9% obtained. These structure refinements demonstrate that Li3N can be considered as an ionic crystal in which the N3- ion, though unstable as a free ion, is stabilized by the surrounding Li+ ions.
High-flux micro-resonators for X-ray and γ-ray lasers
Authors: Denne W. A.
Published: July 2002

It is shown that a small single crystal may resonate at a wide range of X- and γ-ray frequencies. Such a resonator should produce roughly 1011 times greater radiative flux density per photon than previous designs.
Assessment of electron crystallographic data obtained from two-dimensional crystals of biological specimens
Authors: Unger Vinzenz M.
Published: July 2002

Over the past few years, an increasing number of electron crystallographic studies using two-dimensional crystals have shed light on the structure of biologically important macromolecules. Steady progress in the development of specimen-preparation techniques and image-processing tools enable researchers to achieve resolutions in the range of 5–10 Å almost routinely. However, reaching near-atomic resolution remains a formidable task that is likely to require several years. Without doubt, this process will become far less time-consuming as methods are improved further. However, the immediate future is more likely to be dominated by structures solved to an intermediate level of resolution. Since the reliability of such structures is more difficult to assess than that of density maps at near-atomic resolution and as the popularity of electron cryo-microscopy increases it becomes more important to define standardized criteria for the evaluation of electron crystallographic data. This article discusses some of the relevant issues with the aim of stimulating further discussion about the assessment and presentation of electron crystallographic data.
Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps
Authors: Vagin Alexei A. , Isupov Michail N.
Published: July 2002

The molecular-replacement method has been extended to locate molecules and their fragments in an electron-density map. The approach is based on a new spherically averaged phased translation function. The position of the centre of mass of a search model is found prior to determination of its orientation. The orientation is subsequently found by a phased rotation function. The technique also allows superposition of distantly related macromolecules. The method has been implemented in a computer program MOLREP and successfully tested using experimental data sets.
ARP/wARP and molecular replacement
Authors: Perrakis Anastassis , Harkiolaki Maria , Wilson Keith S. , Lamzin Victor S.
Published: July 2002

The aim of ARP/wARP is improved automation of model building and refinement in macromolecular crystallography. Once a molecular-replacement solution has been obtained, it is often tedious to refine and rebuild the initial (search) model. ARP/wARP offers three options to automate that task to varying extents: (i) autobuilding of a completely new model based on phases calculated from the molecular-replacement solution, (ii) updating of the initial model by atom addition and deletion to obtain an improved map and (iii) docking of a structure onto a new (or mutated) sequence, followed by rebuilding and refining the side chains in real space. A few examples are presented where ARP/wARP made a considerable difference in the speed of structure solution and/or made possible refinement of otherwise difficult or uninterpretable maps. The resolution range allowing complete autobuilding of protein structures is currently 2.0 Å, but for map improvement considerable advances over more conventional refinement techniques are evident even at 3.2 Å spacing.
Crystallization and preliminary X-ray diffraction studies of a family 26 endo-β-1,4 mannanase (ManA) from Pseudomonas fluorescens subspecies cellulosa
Authors: Scott M. , Pickersgill R. W. , Hazlewood G. P. , Bolam D. , Gilbert H. J. , Harris G. W.
Published: July 2002

Crystals of an endo-β-1,4-mannanase (1,4-\beta-D-mannohydrolase, E.C. 3.2.1.78) from Pseudomonas fluorescens sub species cellulosa have been grown by the hanging-drop technique at 291 K over a period of one to two weeks to maximal dimensions of 0.17 × 0.17 × 0.25 mm. These crystals belong to the space group R32 (or R3) with cell dimensions of a = b = 155.4 and c = 250.8 Å (hexagonal setting) and contain three (six) molecules in the asymmetric unit. The crystals diffract to at least 3.2 Å using a laboratory source and are suitable for structure determination.
1.2 Å Refinement of the Kunitz-Type Domain from the α3 Chain of Human Type VI Collagen
Authors: Merigeau Karine , Arnoux Bernadette , Perahia David , Norris Kjeld , Norris Fanny , Ducruix Arnaud
Published: July 2002

The recombinant Kunitz-type domain (C5) of human collagen α3(VI) chain was previously described at 1.6 Å resolution at room temperature. By changing the crystallization conditions and using synchrotron radiation, we are able to record diffraction data to 1.2 Å resolution for crystals of the same space group at 291 K. The protein–water–ion model has been refined anisotropically against these new data using the program SHELXL93; the results converged to an R factor of 15.0%, with all data between 7 and 1.2 Å. The final electron-density map reveals a clear chain tracing with a few disordered residues and five residues out of 58 that present alternate conformations. The Cys14–Cys38 bond presents the less frequently observed left-hand conformation (\chi_1 = −60°). The solvent molecules and a phosphate ion are well ordered with an average B of 38 Å2. The high-resolution structure reveals the N and C termini which were missing from the 1.6 Å structure.
Structure Refinement Against Synchrotron Laue Data: Strategies for Data Collection and Reduction
Authors: Yang Xiaojing , Ren Zhong , Moffat Keith
Published: July 2002

The synchrotron Laue technique has been applied to high-resolution structure refinement of the ribotoxin, restrictocin [Yang & Moffat (1996). Structure, 4, 837–852]. By employing carefully designed data-collection strategies and the data-reduction algorithms incorporated in the software system LaueView [Ren & Moffat (1995a). J. Appl. Cryst.
28, 461–481; Ren & Moffat (1995b). J. Appl. Cryst.
28, 482–493], a set of high-resolution Laue data with a completeness and accuracy comparable to excellent monochromatic data was obtained. Through detailed comparison with the monochromatic data and electron-density maps derived from the Laue data, optimum data-collection and reduction strategies were identified and the application of Laue diffraction techniques to conventional crystallographic refinement was demonstrated.
Crystallization of ovine placental lactogen in a 1:2 complex with the extracellular domain of the rat prolactin receptor
Authors: Christinger Hans W. , Elkins Patricia A. , Sandowski Yael , Sakal Edna , Gertler Arieh , Kossiakoff Anthony A. , de Vos Abraham M.
Published: July 2002

Growth hormone and prolactin control somato-lactogenic biology. While high-resolution crystal structures have been determined for receptor complexes of human growth hormone, no such information exists for prolactin. A stable 1:2 complex was formed between ovine placental lactogen, a close prolactin homologue, and two copies of the extracellular portion of the rat prolactin receptor. Using synchrotron radiation, native data have been collected to 2.3 Å. Crystals contain one complex per asymmetric unit. The crystal structure of this complex will shed light on the structural reasons for cross-reactivity and specificity among the endocrine hormones, placental lactogen, prolactin and growth hormone.
SCOP, Structural Classification of Proteins Database: Applications to Evaluation of the Effectiveness of Sequence Alignment Methods and Statistics of Protein Structural Data
Authors: Hubbard Tim J. P. , Ailey Bart , Brenner Steven E. , Murzin Alexey G. , Chothia Cyrus
Published: July 2002

The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop.mrc-lmb.cam.ac.uk/scop/.
Refinement and structural analysis of barnase at 1.5 Å resolution
Authors: Martin Carole , Richard Valerie , Salem Michele , Hartley Robert , Mauguen Yves
Published: July 2002

The structure of Bacillus amyloliquefaciens ribonuclease (barnase), an extracellular 110-residue enzyme initially solved at 2.0 Å resolution, has been refined at 1.5 Å using synchrotron radiation and an imaging-plate scanner. Refinement with anisotropic atomic displacement parameters resulted in increased accuracy of the structure. The final model has a crystallographic R factor of 11.5% and an R
free of 17.4%. The three independent molecules in the asymmetric unit, referred to as A, B and C, allowed detailed analysis of this final model and meaningful comparison with structures of barnase complexed either with nucleotide inhibitors or with its natural intracellular inhibitor, barstar. The analysis of the overall solvent structure revealed a similar number of water molecules associated with each barnase molecule; among these were 16 equivalent buried solvent molecules, the locations of which are discussed in detail and classified on the basis of their structural role. The importance of the water molecules' contribution to the barnase–barstar interaction is also highlighted. The high accuracy of the present analysis revealed the presence of a Zn2+ ion mediating the contacts between pairs of symmetry-related A, B or C molecules; such an ion had previously only been identified for pairs of C molecules.
Purification, crystallization and preliminary X-ray crystallographic analysis of recombinant murine Golgi mannosidase IA, a class I α-mannosidase involved in Asn-linked oligosaccharide maturation
Authors: Vallée Francois , Lal Anita , Moremen Kelley W. , Howell P. Lynne
Published: July 2002

Golgi mannosidase IA is a class I α-mannosidase which catalyzes the conversion of Man9GlcNAc2 or Man8GlcNAc2 oligosaccharide substrates to Man5GlcNAc2 during the maturation of Asn-linked oligosaccharides. The enzyme is a type II membrane protein, and a recombinant form of mannosidase IA from mouse, lacking the transmembrane domain, has been expressed in Pichia pastoris, purified to homogeneity and crystallized by the hanging-drop vapor-diffusion method. The crystals grow as thin rods, with unit-cell dimensions a = 54.9, b = 135.01, c = 69.9 Å. The crystals exhibit the symmetry of space group P2221 and diffract to 2.8 Å resolution. The asymmetric unit contains one monomer (∼53 kDa) and has a solvent content of 59%.
Crystallization and preliminary X-ray analysis of α-D-glucuronidase from Bacillus stearothermophilus T-6
Authors: Teplitsky Anna , Shulami Smadar , Moryles Sara , Zaide Galia , Shoham Yuval , Shoham Gil
Published: July 2002

α-D-Glucuronidases cleave the α-1,2-glycosidic bond of the 4-O-methyl-α-D-glucuronic acid side chain in xylan. Of the xylan-debranching hydrolases, these enzymes are the least studied and characterized. The α-glucuronidase gene (aguA) from Bacillus stearothermophilus T-6 has been cloned, sequenced and overproduced in Escherichia coli. The gene encodes for a protein of 679 amino acids with a calculated molecular weight of 78480 and a pI of 5.42. α-Glucuronidase T-6 shows high homology to the α-glucuronidases of Thermotoga maritima (60% identity) and of Trichoderma reesei (44% identity). Based on the amino-acid sequence similarity, it is likely that these enzymes represent a new class of glycosyl hydrolases. Crystallographic studies of α-glucuronidase T-6 were initiated to study the mechanism of catalysis, as well as to provide a structural basis for rational introduction of enhanced thermostability by site-specific mutagenesis. In this report, the crystallization and preliminary crystallographic characterization of the native α-glucuronidase T-6 enzyme is described. Two crystal forms were found suitable for detailed crystal structure analysis. The T1 form was obtained by the vapour-diffusion method using PEG 4000 as a precipitant and 2-propanol as an organic additive. The crystals belong to a primitive tetragonal crystal system (space group P41212 or P43212) with unit-cell dimensions a = b = 76.1 and c = 331.2 Å. These crystals are mechanically strong, are stable in the X-ray beam and diffract X-rays to better than 2.4 Å resolution. A full 3.0 Å resolution diffraction data set (97.3% completeness, R
merge 9.8%) has recently been collected on one crystal at room temperature using a rotating-anode X-ray source and an R-AXIS IIc imaging-plate detector. The M1 form was obtained and characterized by similar techniques. The best crystallization occurred at a slightly lower pH and a lower concentration of 2-propanol. The crystals belong to a primitive monoclinic crystal system (space group P21) with unit-cell dimensions a = 65.8, b = 127.4, c = 96.6 Å and β = 97.9°. These crystals are also quite strong and stable, and diffract to better than 2.8 Å resolution. A full 2.8 Å resolution diffraction data set (96.2% completeness, R
merge 7.6%) has recently been collected on one crystal at room temperature using the same R-AXIS IIc setup. Both forms are currently being used to obtain crystallographic phasing via isomorphous heavy-atom derivatives and selenomethionine MAD experiments.
Purification, characterization, crystallization and preliminary X-ray diffraction of acuthrombin-B, a thrombin-like enzyme from Agkistrodon acutus venom
Authors: Liu Si-jiu , Huang Qing-qiu , Zhu Xue-yong , Teng Mai-kun , Niu Li-wen
Published: July 2002

Acuthrombin-B, a thrombin-like enzyme from Agkistrodon acutus venom, has been isolated and purified to homogeneity by ion-exchange chromatography on DEAE-Sepharose, gel filtration on Sephacryl S-100 and fast performance liquid chromatography on DEAE-8HR. The protease is an acid protein (pI 6.0) consisting of two non-identical polypeptide chains (14.4 and 16 kDa) and there is no disulfide bond between the subunits. Its molecular weight is 27 kDa as estimated by gel filtration on Sephacryl S-100. The protease has arginine-esterase activity and hydrolyzes synthetic substrates such as p-toluenesulfonyl arginine methyl ester and α-N-benzoyl-L-arginine amide ethyl ester, and shows clotting activity with human fibrinogen, rabbit citrated plasma and human citrated plasma in vitro. The specific activity with human fibrinogen was estimated to be 230 NIH units mg−1. The protease is considered as a serine-type protease and contains metal ion(s) to some extent, as indicated by the fact that its clotting and arginine-esterase activities could be completely inhibited by PMSF and partially inhibited by the chelating agent EDTA, while the thrombin inhibitor heparin had no effect on its clotting activity towards rabbit citrated plasma. Acuthrombin-B crystals with a resolution limit of 2.06 Å were obtained by conventional hanging-drop vapour diffusion. The crystals belong to space group P21 with unit-cell parameters a = 34.97, b = 53.58, c = 67.88 Å, β = 98.89° and contain one molecule per asymmetric unit.
Crystallization and preliminary X-ray diffraction analysis of a biologically active fragment of CD55
Authors: Lea S. , Powell R. , Evans D.
Published: July 2002

Crystals have been grown of two of the domains of CD55. This is the first report of crystallization of a short consensus repeat (SCR) domain containing protein. CD55 is a widely expressed polymorphic glycoprotein, which functions as a complement regulator by inhibiting assembly and promoting destruction of C3 and C5 convertases. As a key regulator of complement, CD55 is implicated in the hyperacute rejection of xenografts from pigs into primates. It is also commonly hijacked as a receptor by viruses (e.g. medically important echoviruses and coxsackieviruses) and bacterial pathogens (e.g. certain pathogenic strains of Escherichia coli). Here, crystallization of a virus-binding fragment expressed in yeast, consisting of two of the four extracellular SCR domains of CD55, is reported. The recombinant domains have been crystallized in 30% polyethylene glycol (PEG), 0.2 M sodium acetate, 0.1 M sodium acetate trihydrate pH 4.6 using the sitting-drop vapour-diffusion method. Two crystal forms are observed (orthorhombic and monoclinic) and a native data set to 1.65 Å resolution has been collected from the monoclinic form at the Synchrotron Radiation Source, Daresbury, UK.
Crystallization and preliminary X-ray crystallographic analysis of a periplasmic tetrahaem flavocytochrome c
3 from Shewanella frigidimarina NCIMB400 which has fumarate reductase activity
Authors: Bamford Vicki , Dobbin Paul S. , Lee Sor-cheng , Reilly Ann , Powell Anne K. , Richardson David J. , Hemmings Andrew M.
Published: July 2002

The fumarate reductase of Escherichia coli and other bacteria is a membrane-bound enzyme consisting of four subunits. A soluble periplasmic 64 kDa tetrahaem flavocytochrome c
3 from Shewanella frigidimarina NCIMB400 which possesses a catalytic fumarate reductase activity has been crystallized. The crystals belong to space group P212121 with unit-cell parameters a = 72.4, b = 110.1, c = 230.2 Å. Assuming a molecular dimer in the asymmetric unit, the crystals contain 65% solvent and, when cryocooled to 100 K, the crystals diffract to at least 3.0 Å resolution. The crystals, however, display an inherent lack of isomorphism and the plausibility of a MAD phasing experiment has therefore been investigated by measuring the iron K absorption edge from a single crystal.
Cubic crystals of phosphopantetheine adenylyltransferase from Escherichia coli
Authors: Izard Tina , Geerlof Arie , Lewendon Ann , Barker John J.
Published: July 2002

Phosphopantetheine adenylyltransferase (PPAT, E.C. 2.7.7.3) catalyzes the penultimate step in coenzyme A (CoA) biosynthesis, transferring an adenylyl group from ATP to 4′-phosphopantetheine, and forming dephospho-CoA. Cubic crystals of native PPAT from Escherichia coli as well as PPAT in complex with its substrates were obtained. The crystals belong to space group I23 or I213 with unit-cell dimension a = 135.5 Å. The crystals diffract to better than 1.8 Å resolution on a Cu Kα rotating-anode generator. The asymmetric unit is likely to contain two molecules, corresponding to a packing density of 2.9 Å3 Da−1.
Crystallization and preliminary diffraction studies of the RNA polymerase subunit RPB5 from Saccharomyces cerevisiae
Authors: Hodach Meredith , Todone Flavia , Eloranta Jyrki J. , Onesti Silvia , Weinzierl Robert O. J.
Published: July 2002

Crystals of the RNA polymerase subunit RPB5 from Saccharomyces cerevisiae have been obtained by vapour-diffusion techniques. The protein has been overexpressed in bacterial cells as a fusion with glutathione S-transferase. Two monoclinic crystal forms can be grown under different sets of conditions. In both cases, the diffraction is consistent with space group P21, with unit-cell parameters a = 45.3, b = 135.3, c = 47.3 Å, β = 118.6° for crystal form I and a = 48.4, b = 137.1, c = 47.1 Å, β = 118.6° for crystal form II.
Crystallization of Helix pomatia agglutinin (HPA), a protein from the edible snail
Authors: Lisgarten John N. , Pitts James E. , Palmer Rex A. , Reynolds Colin D. , Dao-Thi Minh Hoa , Van Driessche Edilbert , Beeckmans Sonia
Published: July 2002

Crystals of Helix pomatia agglutinin (HPA) have been grown by the hanging-drop technique using polyethylene glycol as the precipitant at 293 K. Over a period of one to two weeks the crystals grew to maximum dimensions of 0.10 × 0.05 × 0.02 mm. The crystals belong to space group P6322, with unit-cell dimensions a = b = 63.3, c = 105.2 Å and Z = 12 identical monomers of Mr
= 13 kDa, aggregating into two 78 kDa hexameric protein molecules per unit cell, each with symmetry 32 (D
3). The diffraction pattern extends to 3.6 Å at 293 K.
Cool data: quantity AND quality
Authors: Garman Elspeth
Published: July 2002

The use of cryo-techniques in macromolecular crystallography has increased enormously over the last eight years and has become a vital part of modern X-ray data-collection methods. This paper presents some reasons for the rise in popularity of cryo-techniques and a brief outline of the basic methods, followed by a detailed discussion of factors to be considered when trying to optimize both the quantity and quality of the data collected. As more experimenters at synchrotrons observe significant radiation damage to crystals held near 100 K, the available options for further prolonging crystal lifetime and extending the techniques become worth investigating. Some possibilities and parameters to be considered are presented, although these must remain speculative until more experimental data are available.
Purification, crystallization and preliminary crystallographic study of a Kunitz-type trypsin inhibitor from Delonix regia seeds
Authors: Polikarpov I. , Golubev A. M. , Perles L. A. , Pando S. C. , Novello J. C. , Marangoni S.
Published: July 2002

The Kunitz-type trypsin inhibitor from seeds of Flamboyant (Delonix regia) has been purified to homogeneity and plate-like crystals suitable for X-ray analysis have been grown by the hanging-drop method using PEG 6000 as a precipitant. The crystals belong to space group P212121 with unit-cell parameters a = 32.15, b = 69.39, c = 72.54 Å. X-ray diffraction data have been collected to 2.95 Å resolution. The structure has been solved by molecular replacement using the known structures of trypsin inhibitors from Erythrina caffra seeds (PDB code 1tie) and from soya beans (Glycine max; PDB code 1ba7) as search models.
Purification, solution properties and crystallization of SIV integrase containing a continuous core and C-terminal domain
Authors: Li Ying , Yan Youwei , Zugay-Murphy Joan , Xu Bei , Cole James L. , Witmer Marc , Felock Peter , Wolfe Abigail , Hazuda Daria , Sardana Mohinder K. , Chen Zhongguo , Kuo Lawrence C. , Sardana Vinod V.
Published: July 2002

The C-terminal two-thirds segment of integrase derived from the simian immunodeficiency virus has been cloned, expressed in Escherichia coli, and purified to greater than 95% homogeneity. The protein encompasses amino-acid residues 50–293 and contains a F185H substitution to enhance solubility. In dilute solutions at concentrations below 1 mg ml−1, the enzyme is predominantly dimeric. At the higher concentrations (>10 mg ml−1) required to enable crystallization, the enzyme self-associates to form species with molecular weights greater than 200 kDa. Despite the apparent high aggregation in solution, the enzyme crystallizes from a 8%(v/v) polyethylene glycol (molecular weight 6000) solution in a form suitable for X-ray diffraction studies. The resulting single crystals belong to the space group P212121, with unit-cell parameters a = 79.76, b = 99.98, c = 150.2 Å, α = β = γ = 90° and Z = 4. Under X-ray irradiation generated with a rotating-anode generator, the crystals diffract to 2.8 Å resolution and allow collection of a native 3 Å resolution diffraction data set.
Crystallization and preliminary X-ray diffraction studies of hyperthermostable glutamate dehydrogenase from Thermococcus profundus
Authors: Higuchi Sadaharu , Nakasako Masayoshi , Kudo Toshiaki
Published: July 2002

Recombinant glutamate dehydrogenase from a hyperthermophilic archaeon, Thermococcus profundus, was crystallized in the presence of both polyethylene glycol 8000 and lithium sulfate. Four types of crystals having different morphologies appeared in the crystallization trials; however, only one type was suitable for X-ray crystal structure analysis. The crystal belonged to the monoclinic space group P21 and the unit-cell parameters were a = 112.99, b = 163.70, c = 133.07 Å, β = 113.46° at 110 K. The calculated VM
value of 3.42 Å3 Da−1 was acceptable when one hexamer of the enzyme, which was the physiological functional unit, occupied a crystallographic asymmetric unit. X-ray diffraction intensity data were collected to a resolution of 2.25 Å with good statistics at the BL44B2 beamline of SPring-8.