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  • International Union of Crystallography (IUCr)
  • 2010-2014  (32)
  • 1985-1989  (6,250)
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  • 1
    Publication Date: 2014-04-08
    Description: Human carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the hydration and dehydration of CO2 and HCO3−, respectively. The reaction follows a ping-pong mechanism, in which the rate-limiting step is the transfer of a proton from the zinc-bound solvent (OH−/H2O) in/out of the active site via His64, which is widely believed to be the proton-shuttling residue. The decreased catalytic activity (∼20-fold lower with respect to the wild type) of a variant of CA II in which His64 is replaced with Ala (H64A CA II) can be enhanced by exogenous proton donors/acceptors, usually derivatives of imidazoles and pyridines, to almost the wild-type level. X-ray crystal structures of H64A CA II in complex with four imidazole derivatives (imidazole, 1-methylimidazole, 2-methylimidazole and 4-methylimidazole) have been determined and reveal multiple binding sites. Two of these imidazole binding sites have been identified that mimic the positions of the `in' and `out' rotamers of His64 in wild-type CA II, while another directly inhibits catalysis by displacing the zinc-bound solvent. The data presented here not only corroborate the importance of the imidazole side chain of His64 in proton transfer during CA catalysis, but also provide a complete structural understanding of the mechanism by which imidazoles enhance (and inhibit when used at higher concentrations) the activity of H64A CA II.
    Keywords: human carbonic anhydraseH64Aactivity enhancementrescueactivationimidazole
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 2
    Publication Date: 2014-04-08
    Description: Phosphatases function in the production, transport and recycling of inorganic phosphorus, which is crucial for cellular metabolism and bioenergetics, as well as in bacterial killing, since they are able to generate reactive oxygen species via Fenton chemistry. Diphosphonucleotide phosphatase/phosphodiesterase (PPD1), a glycoprotein plant purple acid phosphatase (PAP) from yellow lupin seeds, contains a bimetallic Fe–Mn catalytic site which is most active at acidic pH. Unlike other plant PAPs, PPD1 cleaves the pyrophosphate bond in diphosphonucleotides and the phosphodiester bond in various phosphodiesters. The homohexameric organization of PPD1, as revealed by a 1.65 Å resolution crystal structure and confirmed by solution X-ray scattering, is unique among plant PAPs, for which only homodimers have previously been reported. A phosphate anion is bound in a bidentate fashion at the active site, bridging the Fe and Mn atoms in a binding mode similar to that previously reported for sweet potato PAP, which suggests that common features occur in their catalytic mechanisms. The N-terminal domain of PPD1 has an unexpected and unique fibronectin type III-like fold that is absent in other plant PAPs. Here, the in vitro DNA-cleavage activity of PPD1 is demonstrated and it is proposed that the fibronectin III-like domain, which `overhangs' the active site, is involved in DNA selectivity, binding and activation. The degradation of DNA by PPD1 implies a role for PPD1 in plant growth and repair and in pathogen defence.
    Keywords: purple acid phosphatasediphosphonucleotide phosphatasephosphodiesterasePPD1bimetallic Fe–Mnfibronectin type III domaincrystal structureSAXS
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 3
    Publication Date: 2014-04-08
    Description: Acemetacin (ACM) is a non-steroidal anti-inflammatory drug (NSAID), which causes reduced gastric damage compared with indomethacin. However, acemetacin has a tendency to form a less soluble hydrate in the aqueous medium. We noted difficulties in the preparation of cocrystals and salts of acemetacin by mechanochemical methods, because this drug tends to form a hydrate during any kind of solution-based processing. With the objective to discover a solid form of acemetacin that is stable in the aqueous medium, binary adducts were prepared by the melt method to avoid hydration. The coformers/salt formers reported are pyridine carboxamides [nicotinamide (NAM), isonicotinamide (INA), and picolinamide (PAM)], caprolactam (CPR), p-aminobenzoic acid (PABA), and piperazine (PPZ). The structures of an ACM–INA cocrystal and a binary adduct ACM–PABA were solved using single-crystal X-ray diffraction. Other ACM cocrystals, ACM–PAM and ACM–CPR, and the piperazine salt ACM–PPZ were solved from high-resolution powder X-ray diffraction data. The ACM–INA cocrystal is sustained by the acid...pyridine heterosynthon and N—H...O catemer hydrogen bonds involving the amide group. The acid...amide heterosynthon is present in the ACM–PAM cocrystal, while ACM–CPR contains carboxamide dimers of caprolactam along with acid–carbonyl (ACM) hydrogen bonds. The cocrystals ACM–INA, ACM–PAM and ACM–CPR are three-dimensional isostructural. The carboxyl...carboxyl synthon in ACM–PABA posed difficulty in assigning the position of the H atom, which may indicate proton disorder. In terms of stability, the salts were found to be relatively stable in pH 7 buffer medium over 24 h, but the cocrystals dissociated to give ACM hydrate during the same time period. The ACM–PPZ salt and ACM–nicotinamide cocrystal dissolve five times faster than the stable hydrate form, whereas the ACM–PABA adduct has 2.5 times faster dissolution rate. The pharmaceutically acceptable piperazine salt of acemetacin exhibits superior stability, faster dissolution rate and is able to overcome the hydration tendency of the reference drug.
    Keywords: cocrystalhydratemelt crystallizationpiperazinepowder X-ray diffractionstructure determination from powder data (SDPD)
    Electronic ISSN: 2052-2525
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  • 4
    Publication Date: 2014-04-08
    Description: Crystal structure determinations of biological macromolecules are limited by the availability of sufficiently sized crystals and by the fact that crystal quality deteriorates during data collection owing to radiation damage. Exploiting a micrometre-sized X-ray beam, high-precision diffractometry and shutterless data acquisition with a pixel-array detector, a strategy for collecting data from many micrometre-sized crystals presented to an X-ray beam in a vitrified suspension is demonstrated. By combining diffraction data from 80 Trypanosoma brucei procathepsin B crystals with an average volume of 9 µm3, a complete data set to 3.0 Å resolution has been assembled. The data allowed the refinement of a structural model that is consistent with that previously obtained using free-electron laser radiation, providing mutual validation. Further improvements of the serial synchrotron crystallography technique and its combination with serial femtosecond crystallography are discussed that may allow the determination of high-resolution structures of micrometre-sized crystals.
    Keywords: protein microcrystallographyserial crystallographyin vivo grown microcrystals
    Electronic ISSN: 2052-2525
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  • 5
    Publication Date: 2014-04-08
    Description: X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.
    Keywords: two-dimensional protein crystalfemtosecond crystallographysingle layer X-ray diffractionmembrane protein
    Electronic ISSN: 2052-2525
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  • 6
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-04-08
    Keywords: biological crystallographyeditorialIUCrJ
    Electronic ISSN: 2052-2525
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  • 7
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-04-08
    Keywords: protein microcrystallographyserial crystallographyin vivo-grown microcrystals
    Electronic ISSN: 2052-2525
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  • 8
    Publication Date: 2014-04-08
    Description: The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals, such as 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole [Paul, Kubicki, Jelsch et al. (2011). Acta Cryst. B67, 365–378], it may not be sufficient for a correct description of the charge-density distribution. Multipole refinement using harmonic atom vibrations does not lead to the best electron density model in this case and the so-called `shashlik-like' pattern of positive and negative residual electron density peaks is observed in the vicinity of some atoms. This slight disorder, which cannot be modelled by split atoms, was solved using third-order anharmonic nuclear motion (ANM) parameters. Multipole refinement of the experimental high-resolution X-ray diffraction data of 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole at three different temperatures (10, 35 and 70 K) and a series of powder diffraction experiments (20 ≤ T ≤ 300 K) were performed to relate this anharmonicity observed for several light atoms (N atoms of amino and nitro groups, and O atoms of nitro groups) to an isomorphic phase transition reflected by a change in the b cell parameter around 65 K. The observed disorder may result from the coexistence of domains of two phases over a large temperature range, as shown by low-temperature powder diffraction.
    Keywords: anharmonicityisomorphic phase transitionexperimental charge densityX-ray closed-circuit helium cryostatHansen–Coppens modelmultiple-temperature powder diffraction
    Electronic ISSN: 2052-2525
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  • 9
    Publication Date: 2014-04-08
    Description: The partitioning of space with Hirshfeld surfaces enables the analysis of fingerprint molecular interactions in crystalline environments. This study uses the decomposition of the crystal contact surface between pairs of interacting chemical species to derive an enrichment ratio. This quantity enables the analysis of the propensity of chemical species to form intermolecular interactions with themselves and other species. The enrichment ratio is obtained by comparing the actual contacts in the crystal with those computed as if all types of contacts had the same probability to form. The enrichments and contact tendencies were analyzed in several families of compounds, based on chemical composition and aromatic character. As expected, the polar contacts of the type H...N, H...O and H...S, which are generally hydrogen bonds, show enrichment values larger than unity. O...O and N...N contacts are impoverished while H...H interactions display enrichment ratios which are generally close to unity or slightly lower. In aromatic compounds, C...C contacts can display large enrichment ratios due to extensive π...π stacking in the crystal packings of heterocyclic compounds. C...C contacts are, however, less enriched in pure (C,H) hydrocarbons as π...π stacking is not so favourable from the electrostatic point of view compared with heterocycles. C...H contacts are favoured in (C,H) aromatics, but these interactions occur less in compounds containing O, N or S as some H atoms are then involved in hydrogen bonds. The study also highlights the fact that hydrogen is a prefered interaction partner for fluorine.
    Keywords: enrichment ratioHirshfeld surface analysiscrystal packingfingerprint plots
    Electronic ISSN: 2052-2525
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  • 10
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Keywords: Editorialchemical crystallographycrystal engineering
    Electronic ISSN: 2052-2525
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  • 11
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: The crystallographic structure solution of nucleotides and nucleotide complexes is now commonplace. The resulting electron-density maps are often poorer than for proteins, and as a result interpretation in terms of an atomic model can require significant effort, particularly in the case of large structures. While model building can be performed automatically, as with proteins, the process is time-consuming, taking minutes to days depending on the software and the size of the structure. A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software, with extended chain fragments built around the current view position in a fraction of a second. The speed of the method arises from the determination of the `fingerprint' of the sugar and phosphate groups in terms of conserved high-density and low-density features, coupled with a highly efficient scoring algorithm. Use cases include the rapid evaluation of an initial electron-density map, addition of nucleotide fragments to prebuilt protein structures, and in favourable cases the completion of the structure while automated model-building software is still running. The method has been incorporated into the Coot software package.
    Keywords: nucleic acid chain tracingCoot
    Electronic ISSN: 2052-2525
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  • 12
    Publication Date: 2014-11-12
    Description: Accurate structural models of reaction centres in zeolite catalysts are a prerequisite for mechanistic studies and further improvements to the catalytic performance. The Rietveld/maximum entropy method is applied to synchrotron powder X-ray diffraction data on fully dehydrated CHA-type zeolites with and without loading of catalytically active Cu2+ for the selective catalytic reduction of NOx with NH3. The method identifies the known Cu2+ sites in the six-membered ring and a not previously observed site in the eight-membered ring. The sum of the refined Cu occupancies for these two sites matches the chemical analysis and thus all the Cu is accounted for. It is furthermore shown that approximately 80% of the Cu2+ is located in the new 8-ring site for an industrially relevant CHA zeolite with Si/Al = 15.5 and Cu/Al = 0.45. Density functional theory calculations are used to corroborate the positions and identity of the two Cu sites, leading to the most complete structural description of dehydrated silicoaluminate CHA loaded with catalytically active Cu2+ cations.
    Keywords: CHA zeolitescatalytic activitylocation of Cu2+synchrotron powder X-ray diffractionRietveld/maximum entropy method
    Electronic ISSN: 2052-2525
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  • 13
    Publication Date: 2014-11-12
    Description: Crystallographic auto-indexing algorithms provide crystal orientations and unit-cell parameters and assign Miller indices based on the geometric relations between the Bragg peaks observed in diffraction patterns. However, if the Bravais symmetry is higher than the space-group symmetry, there will be multiple indexing options that are geometrically equivalent, and hence many ways to merge diffraction intensities from protein nanocrystals. Structure factor magnitudes from full reflections are required to resolve this ambiguity but only partial reflections are available from each XFEL shot, which must be merged to obtain full reflections from these `stills'. To resolve this chicken-and-egg problem, an expectation maximization algorithm is described that iteratively constructs a model from the intensities recorded in the diffraction patterns as the indexing ambiguity is being resolved. The reconstructed model is then used to guide the resolution of the indexing ambiguity as feedback for the next iteration. Using both simulated and experimental data collected at an X-ray laser for photosystem I in the P63 space group (which supports a merohedral twinning indexing ambiguity), the method is validated.
    Keywords: indexing ambiguityserial femtosecond crystallography (SFX)XFELsprotein crystallographyexpectation maximization algorithm
    Electronic ISSN: 2052-2525
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  • 14
    Publication Date: 2014-11-12
    Description: The time evolution of the electron density and the resulting time dependence of Fourier components of the X-ray polarizability of a crystal irradiated by highly intense femtosecond pulses of an X-ray free-electron laser (XFEL) is investigated theoretically on the basis of rate equations for bound electrons and the Boltzmann equation for the kinetics of the unbound electron gas. The photoionization, Auger process, electron-impact ionization, electron–electron scattering and three-body recombination have been implemented in the system of rate equations. An algorithm for the numerical solution of the rate equations was simplified by incorporating analytical expressions for the cross sections of all the electron configurations in ions within the framework of the effective charge model. Using this approach, the time dependence of the inner shell populations during the time of XFEL pulse propagation through the crystal was evaluated for photon energies between 4 and 12 keV and a pulse width of 40 fs considering a flux of 1012 photons pulse−1 (focusing on a spot size of ∼1 µm). This flux corresponds to a fluence ranging between 0.8 and 2.4 mJ µm−2. The time evolution of the X-ray polarizability caused by the change of the atomic scattering factor during the pulse propagation is numerically analyzed for the case of a silicon crystal. The time-integrated polarizability drops dramatically if the fluence of the X-ray pulse exceeds 1.6 mJ µm−2.
    Keywords: femtosecond pulseX-ray diffractionpolarizabilityelectron densityrate equations
    Electronic ISSN: 2052-2525
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  • 15
    Publication Date: 2014-11-12
    Description: Melting of native tapioca starch granules in aqueous pastes upon heating is observed in situ using simultaneous small- and wide-angle X-ray scattering (SAXS/WAXS) and solution viscometry. Correlated structure and viscosity changes suggest closely associated amylose and amylopectin chains in the semicrystalline layers, and the release of amylose chains for enhanced solution viscosity occurs largely after melting of the semicrystalline structure. Before melting, WAXS results reveal mixed crystals of A- and B-types (∼4:1 by weight), whereas SAXS results indicate that the semicrystalline layers are composed of lamellar blocklets of ca 43 nm domain size, with polydisperse crystalline (≃7.5 nm) and amorphous (≃1.1 nm) layers alternatively assembled into a lamellar spacing of ≃8.6 nm with 20% polydispersity. Upon melting, the semicrystalline lamellae disintegrate into disperse and molten amylopectin nanoclusters with dissolved and partially untangled amylose chains in the aqueous matrix which leads to increased solution viscosity. During subsequent cooling, gelation starts at around 347 K; successively increased solution viscosity coincides with the development of nanocluster aggregation to a fractal dimension ≃2.3 at 303 K, signifying increasing intercluster association through collapsed amylose chains owing to decreased solvency of the aqueous medium with decreasing temperature.
    Keywords: tapioca starch granulesgelatinizationgelationSAXS/WAXSviscosity
    Electronic ISSN: 2052-2525
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  • 16
    Publication Date: 2014-11-12
    Description: Molecular self-assembly of nylon-12 rods in self-organized nanoporous alumina cylinders with two different diameters (65 and 300 nm) is studied with transmission electron microscopy (TEM) and wide-angle X-ray diffraction (WAXD) in symmetrical reflection mode. In a rod with a 300 nm diameter, the tendency of the hydrogen-bonding direction of a γ-form crystal parallel to the long axis of the rod is not clear because of weak two-dimensional confinement. In a rod with a diameter of 65 nm, the tendency of the hydrogen-bonding direction of a γ-form crystal parallel to the long axis of the rod is more distinct because of strong two-dimensional confinement. For the first time, selected-area electron diffraction (SAED) is applied in a transmission electron microscope to a polymer nanorod in order to determine the hydrogen-bond sheet and lamellar orientations. Results of TEM–SAED and WAXD showed that the crystals within the rod possess the γ-form of nylon-12 and that the b axis (stem axis) of the γ-form crystals is perpendicular to the long axis of the rod. These results revealed that only lamellae with 〈h0l〉 directions are able to grow inside the nanopores and the growth of lamellae with 〈hkl〉 (k ≠ 0) directions is stopped owing to impingements against the cylinder walls. The dominant crystal growth direction of the 65 nm rod in stronger two-dimensional confinement is in between the [−201] and [001] directions due to the development of a hydrogen-bonded sheet restricted along the long axis of the rod.
    Keywords: molecular self-assemblynanorodsselected-area electron diffractioncylindrical confinement
    Electronic ISSN: 2052-2525
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  • 17
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: For more than 30 years X-ray crystallography has been by far the most powerful approach for determining the structures of viruses and viral proteins at atomic resolution. The information provided by these structures, which covers many important aspects of the viral life cycle such as cell-receptor recognition, viral entry, nucleic acid transfer and genome replication, has extensively enriched our vision of the virus world. Many of the structures available correspond to potential targets for antiviral drugs against important human pathogens. This article provides an overview of the current knowledge of different structural aspects of the above-mentioned processes.
    Keywords: bacteriophagesgenome deliveryfusion proteinsRNA-dependent RNA polymerasesviral proteasesviral receptorsviruses
    Electronic ISSN: 2052-2525
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  • 18
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug–receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug–receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
    Keywords: charge-density researchmedicinal chemistrydrug designinvariomHansen–Coppens multipole modelquantum theory of atoms in molecules
    Electronic ISSN: 2052-2525
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  • 19
    Publication Date: 2014-11-12
    Description: Metastable phases are often used to design materials with outstanding properties, which cannot be achieved with thermodynamically stable compounds. In many cases, the metastable phases are employed as precursors for controlled formation of nanocomposites. This contribution shows how the microstructure of crystalline metastable phases and the formation of nanocomposites can be concluded from X-ray diffraction experiments by taking advantage of the high sensitivity of X-ray diffraction to macroscopic and microscopic lattice deformations and to the dependence of the lattice deformations on the crystallographic direction. The lattice deformations were determined from the positions and from the widths of the diffraction lines, the dependence of the lattice deformations on the crystallographic direction from the anisotropy of the line shift and the line broadening. As an example of the metastable system, the supersaturated solid solution of titanium nitride and aluminium nitride was investigated, which was prepared in the form of thin films by using cathodic arc evaporation of titanium and aluminium in a nitrogen atmosphere. The microstructure of the (Ti,Al)N samples under study was tailored by modifying the [Al]/[Ti] ratio in the thin films and the surface mobility of the deposited species.
    Keywords: metastable thin filmsmicrostructureX-ray diffraction
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  • 20
    Publication Date: 2014-11-12
    Description: Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer–monomer interface is more extensive than that at the dimer–dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.
    Keywords: transthyretinamyloid assemblyneutron crystallographydeuteration
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  • 21
    Publication Date: 2014-11-12
    Description: The Mars Science Laboratory landed in Gale crater on Mars in August 2012, and the Curiosity rover then began field studies on its drive toward Mount Sharp, a central peak made of ancient sediments. CheMin is one of ten instruments on or inside the rover, all designed to provide detailed information on the rocks, soils and atmosphere in this region. CheMin is a miniaturized X-ray diffraction/X-ray fluorescence (XRD/XRF) instrument that uses transmission geometry with an energy-discriminating CCD detector. CheMin uses onboard standards for XRD and XRF calibration, and beryl:quartz mixtures constitute the primary XRD standards. Four samples have been analysed by CheMin, namely a soil sample, two samples drilled from mudstones and a sample drilled from a sandstone. Rietveld and full-pattern analysis of the XRD data reveal a complex mineralogy, with contributions from parent igneous rocks, amorphous components and several minerals relating to aqueous alteration. In particular, the mudstone samples all contain one or more phyllosilicates consistent with alteration in liquid water. In addition to quantitative mineralogy, Rietveld refinements also provide unit-cell parameters for the major phases, which can be used to infer the chemical compositions of individual minerals and, by difference, the composition of the amorphous component.
    Keywords: X-ray diffractionMarsextraterrestrial mineralogyCuriosity rover
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  • 22
    Publication Date: 2014-11-12
    Description: Small- and wide-angle X-ray scattering (SAXS, WAXS) are standard tools in materials research. The simultaneous measurement of SAXS and WAXS data in time-resolved studies has gained popularity due to the complementary information obtained. Furthermore, the combination of these data with non X-ray based techniques, via either simultaneous or independent measurements, has advanced understanding of the driving forces that lead to the structures and morphologies of materials, which in turn give rise to their properties. The simultaneous measurement of different data regimes and types, using either X-rays or neutrons, and the desire to control parameters that initiate and control structural changes have led to greater demands on sample environments. Examples of developments in technique combinations and sample environment design are discussed, together with a brief speculation about promising future developments.
    Keywords: SAXSWAXSSANScomplementary techniquessample environment
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  • 23
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: Membranes are amongst the most important biological structures; they maintain the fundamental integrity of cells, compartmentalize regions within them and play an active role in a wide range of cellular processes. Pressure can play a key role in probing the structure and dynamics of membrane assemblies, and is also critical to the biology and adaptation of deep-sea organisms. This article presents an overview of the effect of pressure on the mesostructure of lipid membranes, bilayer organization and lipid–protein assemblies. It also summarizes recent developments in high-pressure structural instrumentation suitable for experiments on membranes.
    Keywords: biological membraneslipidsbilayerslipid–protein assemblieshigh-pressure studies
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  • 24
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: Most properties of nanocrystalline materials are shape-dependent, providing their exquisite tunability in optical, mechanical, electronic and catalytic properties. An example of the former is localized surface plasmon resonance (LSPR), the coherent oscillation of conduction electrons in metals that can be excited by the electric field of light; this resonance frequency is highly dependent on both the size and shape of a nanocrystal. An example of the latter is the marked difference in catalytic activity observed for different Pd nanoparticles. Such examples highlight the importance of particle shape in nanocrystalline materials and their practical applications. However, one may ask `how are nanoshapes created?', `how does the shape relate to the atomic packing and crystallography of the material?', `how can we control and characterize the external shape and crystal structure of such small nanocrystals?'. This feature article aims to give the reader an overview of important techniques, concepts and recent advances related to these questions. Nucleation, growth and how seed crystallography influences the final synthesis product are discussed, followed by shape prediction models based on seed crystallography and thermodynamic or kinetic parameters. The crystallographic implications of epitaxy and orientation in multilayered, core-shell nanoparticles are overviewed, and, finally, the development and implications of novel, spatially resolved analysis tools are discussed.
    Keywords: nanocrystalline materialsplasmonicsshape prediction models
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  • 25
    Publication Date: 2014-11-12
    Description: Membrane fusion is essential for human health, playing a vital role in processes as diverse as neurotransmission and blood glucose control. Two protein families are key: (1) the Sec1p/Munc18 (SM) and (2) the soluble N-ethylmaleimide-sensitive attachment protein receptor (SNARE) proteins. Whilst the essential nature of these proteins is irrefutable, their exact regulatory roles in membrane fusion remain controversial. In particular, whether SM proteins promote and/or inhibit the SNARE-complex formation required for membrane fusion is not resolved. Crystal structures of SM proteins alone and in complex with their cognate SNARE proteins have provided some insight, however, these structures lack the transmembrane spanning regions of the SNARE proteins and may not accurately reflect the native state. Here, we review the literature surrounding the regulatory role of mammalian Munc18 SM proteins required for exocytosis in eukaryotes. Our analysis suggests that the conflicting roles reported for these SM proteins may reflect differences in experimental design. SNARE proteins appear to require C-terminal immobilization or anchoring, for example through a transmembrane domain, to form a functional fusion complex in the presence of Munc18 proteins.
    Keywords: SM proteinsSNARE proteinssyntaxinMunc18membrane trafficking
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 26
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: The biological solution small-angle X-ray scattering (BioSAXS) field has undergone tremendous development over recent decades. This means that increasingly complex biological questions can be addressed by the method. An intricate synergy between advances in hardware and software development, data collection and evaluation strategies and implementations that readily allow integration with complementary techniques result in significant results and a rapidly growing user community with ever increasing ambitions. Here, a review of these developments, by including a selection of novel BioSAXS methodologies and recent results, is given.
    Keywords: biological solution small-angle X-ray scattering (BioSAXS)synchrotron radiationbeamlinesstructural complexitybiostructural research
    Electronic ISSN: 2052-2525
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  • 27
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: The study of single-crystal diffuse scattering (SCDS) goes back almost to the beginnings of X-ray crystallography. Because SCDS arises from two-body correlations, it contains information about local (short-range) ordering in the sample, information which is often crucial in the attempt to relate structure to function. This review discusses the state of the field, including detectors and data collection and the modelling of SCDS using Monte Carlo and ab initio techniques. High-quality, three-dimensional volumes of SCDS data can now be collected at synchrotron light sources, allowing ever more detailed and quantitative analyses to be undertaken, and opening the way to approaches such as three-dimensional pair distribution function studies (3D-PDF) and automated refinement of a disorder model, powerful techniques that require large volumes of low-noise data.
    Keywords: single-crystal diffuse scatteringdisordersynchrotron light sources
    Electronic ISSN: 2052-2525
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  • 28
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: The smart specialization declared in the European program Horizon 2020, and the increasing cooperation between research and development found in companies and researchers at universities and research institutions have created a new paradigm where many calls for proposals require participation and funding from public and private entities. This has created a unique opportunity for large-scale facilities, such as synchrotron research laboratories, to participate in and support applied research programs. Scientific staff at synchrotron facilities have developed many advanced tools that make optimal use of the characteristics of the light generated by the storage ring. These tools have been exceptionally valuable for materials characterization including X-ray absorption spectroscopy, diffraction, tomography and scattering, and have been key in solving many research and development issues. Progress in optics and detectors, as well as a large effort put into the improvement of data analysis codes, have resulted in the development of reliable and reproducible procedures for materials characterization. Research with photons has contributed to the development of a wide variety of products such as plastics, cosmetics, chemicals, building materials, packaging materials and pharma. In this review, a few examples are highlighted of successful cooperation leading to solutions of a variety of industrial technological problems which have been exploited by industry including lessons learned from the Science Link project, supported by the European Commission, as a new approach to increase the number of commercial users at large-scale research infrastructures.
    Keywords: X-ray techniquesindustryinnovation
    Electronic ISSN: 2052-2525
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  • 29
    Publication Date: 2014-11-12
    Description: Iron(II) and 2-oxoglutarate (2OG)-dependent dioxygenases involved in histone and DNA/RNA demethylation convert the cosubstrate 2OG and oxygen to succinate and carbon dioxide, resulting in hydroxylation of the methyl group of the substrates and subsequent demethylation. Recent evidence has shown that these 2OG dioxygenases play vital roles in a variety of biological processes, including transcriptional regulation and gene expression. In this review, the structure and function of these dioxygenases in histone and nucleic acid demethylation will be discussed. Given the important roles of these 2OG dioxygenases, detailed analysis and comparison of the 2OG dioxygenases will guide the design of target-specific small-molecule chemical probes and inhibitors.
    Keywords: dioxygenaseshistone demethylationDNA/RNA demethylationN6-methyladenosineALKBH5
    Electronic ISSN: 2052-2525
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  • 30
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: Worldwide research activity at the nanoscale is triggering the appearance of new, and frequently surprising, materials properties in which the increasing importance of surface and interface effects plays a fundamental role. This opens further possibilities in the development of new multifunctional materials with tuned physical properties that do not arise together at the bulk scale. Unfortunately, the standard methods currently available for solving the atomic structure of bulk crystals fail for nanomaterials due to nanoscale effects (very small crystallite sizes, large surface-to-volume ratio, near-surface relaxation, local lattice distortions etc.). As a consequence, a critical reexamination of the available local-structure characterization methods is needed. This work discusses the real possibilities and limits of X-ray absorption spectroscopy (XAS) analysis at the nanoscale. To this end, the present state of the art for the interpretation of extended X-ray absorption fine structure (EXAFS) is described, including an advanced approach based on the use of classical molecular dynamics and its application to nickel oxide nanoparticles. The limits and possibilities of X-ray absorption near-edge spectroscopy (XANES) to determine several effects associated with the nanocrystalline nature of materials are discussed in connection with the development of ZnO-based dilute magnetic semiconductors (DMSs) and iron oxide nanoparticles.
    Keywords: EXAFSXANESoxide nanomaterialsnanocrystalline materials
    Electronic ISSN: 2052-2525
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  • 31
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: The community of material scientists is strongly committed to the research area of multiferroic materials, both for the understanding of the complex mechanisms supporting the multiferroism and for the fabrication of new compounds, potentially suitable for technological applications. The use of high pressure is a powerful tool in synthesizing new multiferroic, in particular magneto-electric phases, where the pressure stabilization of otherwise unstable perovskite-based structural distortions may lead to promising novel metastable compounds. The in situ investigation of the high-pressure behavior of multiferroic materials has provided insight into the complex interplay between magnetic and electronic properties and the coupling to structural instabilities.
    Keywords: high pressuremultiferroicsmaterials science
    Electronic ISSN: 2052-2525
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  • 32
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2014-11-12
    Description: Metal–organic frameworks (MOFs) are one of the most intensely studied material types in recent times. Their networks, resulting from the formation of strong bonds between inorganic and organic building units, offer unparalled chemical diversity and pore environments of growing complexity. Therefore, advances in single-crystal X-ray diffraction equipment and techniques are required to characterize materials with increasingly larger surface areas, and more complex linkers. In addition, whilst structure solution from powder diffraction data is possible, the area is much less populated and we detail the current efforts going on here. We also review the growing number of reports on diffraction under non-ambient conditions, including the response of MOF structures to very high pressures. Such experiments are important due to the expected presence of stresses in proposed applications of MOFs – evidence suggesting rich and complex behaviour. Given the entwined and inseparable nature of their structure, properties and applications, it is essential that the field of structural elucidation is able to continue growing and advancing, so as not to provide a rate-limiting step on characterization of their properties and incorporation into devices and applications. This review has been prepared with this in mind.
    Keywords: MOFsnon-ambient crystallographycrystal growth
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  • 33
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 182-183 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Easy and convenient techniques have been developed to handle air-sensitive compounds in terms of measuring their single-crystal X-ray diffraction intensities. These methods have also been fruitfully applied in collecting X-ray data of several highly air-sensitive inorganic and organometallic compounds without using a cold stream of nitrogen.
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  • 34
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 187-187 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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  • 35
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 209-215 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Point-defect aggregates in (111) dislocation-free silicon single crystals grown by the float-zone (FZ) method have been studied by diffuse X-ray scattering (DXS) and compared with those in the Czochralski-grown (CZ) crystals. A two-axis X-ray diffractometer was used. It employs three monochromators in (+, −, −) setting to obtain a highly collimated and monochromatic Mo Kα1 beam. DXS measurements were made around the 111 reciprocal-lattice point (r.l.p.) with K* along ±[111] and ±[01{\bar 1}]; K is the vector which joins the elemental volume of the reciprocal space under investigation to the nearest r.l.p. For FZ crystals for a given K* the DXS intensity was higher for θ 〈 θB in comparison with that for θ 〉 θB showing that the anisotropy (DXS Iθ 〉 θB − DXS Iθ 〈 θB) is negative, as expected for vacancy clusters. For CZ crystals the anisotropy was positive, owing to the presence of interstitial clusters. The magnitude of anisotropy in the FZ crystals was smaller than that observed in the CZ crystals. The DXS intensity varies approximately as K−2 near Bragg peaks (Huang scattering) and as K*−4 (Stokes–Wilson scattering) away from it. From the K* values where the changeover from Huang to Stokes–Wilson scattering takes place the size of the clusters assumed to be the origin of the observed DXS is estimated as ̃2 × 10−4 and 2.6 × 10−3 mm for FZ and ̃5.5 × 10−4 and 3 × 10−3 mm for CZ crystals. The experimental data were compared with theoretically calculated DXS distributions assuming the defects to be dislocation loops. The number of point defects in a loop has been estimated.
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  • 36
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 205-208 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The effect of texture on the interpretation of the classical radial distribution function (RDF) is studied. A model of axial texture is presented which enables the calculation of the effect for individual interatomic distances and an analysis of the effect on the global RDF. The example shows that the shift of the RDF closest-neighbour peak position can be as large as 0.06 Å.
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  • 37
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 216-221 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The components of a symmetric second-rank tensor (e.g. the strain tensor) can be calculated from measurements of that tensor property in at least six directions. A system of simultaneous equations (t(m) = Σ6i = 1 amiti) must be solved. The coefficient matrix ami is determined by the measurement directions, and therefore it is of great importance to choose these directions properly. Part 1 deals with the necessary condition: rank (ami)〈〉 0. Rules are given by which it is easy to decide whether rank (ami) = 0 or rank (ami) ≷0 without calculating the rank. In part 2 methods are developed to find optimized sets of measurement directions. An optimized set is one for which the inevitable measurement errors will give errors of the calculated tensor components as small as possible. Special attention is given to the case of X-ray strain measurement of single crystals.
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  • 38
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 308-314 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Following the discovery of systems with diffraction patterns exhibiting icosahedral symmetry by Shechtman, Blecht, Gratias & Cahn [Phys. Rev. Lett. (1984), 53, 1951–1953], which is forbidden in classical crystallography, interest has centred on Penrose tiling and its generalizations as a model for the explanation of these patterns, although Pauling [Nature (London) (1985), 317, 512–514; Phys. Rev. Lett. (1987), 58, 365–368] has proposed an alternative explanation in terms of crystal twinning. In an attempt to reconcile these two points of view a computer algorithm has been developed, following the methods outlined by Wolny, Pytlik & Lebech [J. Phys. C (1988), 21, 2267–2277], to grow a number of different structures which all tile the two-dimensional (2D) plane without defects. With the same two types of basic unit, it is shown that it is possible, on the one hand, to produce structures similar to the Penrose tiling pattern and, on the other, different types of twinned and disordered structures, with a continuous sequence of intermediates. Optical diffraction patterns of these structures have been obtained for comparison with real quasi-crystals.
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  • 39
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 380-380 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Owing to a printer's error, the fourth equation given in the Abstract of the paper by Åsbrink, Kihlborg & Malinowski [J. Appl. Cryst. (1988). 21, 960–962] is incorrect. The correct equation is {\bar \beta}_c(0–7.41 GPa) = −3.35 × 10−4 (GPa)−1.
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  • 40
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 384-387 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: NRCVAX is a complete system of programs, covering all aspects of crystal structure analysis from data reduction to the presentation of results. The system, which is written in a `neutral' Fortran 77, presently exists in two forms. The first runs on a VAX computer under VMS, on an 80386 PC under UNIX and under IBM VM/CMS and MVS/TSO. The second is an adaptation which runs on PC-XT, AT, PS/2 and comparable microcomputers under MS-DOS. The two versions differ somewhat in structure, but very little in code, operation or functionality except for the graphics. The many options of the programs can be selected in a highly interactive manner and because of this the system is very flexible. Most options are assigned default values, however, and it is usually safe to run the routines with a minimum of user input using the defaults. The system will accept data from a wide variety of sources and has interface routines for several other systems. Graphics in the VAX/UNIX version are based on the widely available Tektronix 4000 series protocol, while the microcomputer version supports most common display adapters. It is also possible to prepare files for a variety of plotters, dot-matrix printers and laser printers. Source code is distributed and it should not be difficult to adapt the system to any computer with virtual memory and a Fortran 77 compiler.
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  • 41
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 394-395 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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  • 42
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 396-397 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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  • 43
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 398-400 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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  • 44
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 476-482 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: General considerations are given for the importance of providing an energy/wavelength-dependent database of neutron coherent scattering lengths, and of the possibility of constructing such a base from the range of neutron cross-section data that are generally available for a wide range of nuclides. The case of europium is considered in detail, partly because it is a good example of an element with strong resonance effects in the wavelength region of importance in crystallographic and condensed-matter studies, and partly because it is an exceptional case from the nuclear point of view, having multi-level interference effects. From the available cross-section data the complex coherent scattering length is constructed as a function of neutron energy up to 0.7 eV, for the isotopes and for the natural element. Some single-level approximations for the scattering-length function of 151Eu are given.
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  • 45
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 533-538 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A method is proposed for measuring textures on the surfaces of thin wires. The method is based on a numerical absorption correction analysis of the sample. Analytical formulas are given for thicker or more strongly absorbing specimens. Experimental work is presented to illustrate the use of the method.
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  • 46
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    Applied crystallography online 22 (1989), S. 528-532 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Grazing-incidence small-angle X-ray scattering (GISAXS) is introduced as a method of studying discontinuous thin films. In this method, the incident beam is totally externally reflected from the substrate followed by small-angle scattering of the refracted beam by the thin film. The experiment described establishes the ability of GISAXS to provide size information for islands formed in the initial stages of thin film growth. The data presented are for gold films of 7 and 15 Å average thicknesses on Corning 7059 glass substrates. The advantages of this technique are that it is non-destructive, can be done in situ, provides excellent sampling statistics, does not necessarily require a synchrotron source, and is not limited to thin or conducting substrates.
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  • 47
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    Applied crystallography online 22 (1989), S. 559-561 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Series-expansion coefficients for an orientation distribution function (ODF) of cold-rolled aluminium sheet were calculated from the intensity of Debye–Scherrer rings obtained in an experiment using synchrotron radiation. Calculated and observed pole figures demonstrate that a sufficiently good approximation to the ODF is obtained from coefficients calculated to l = 8.
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  • 48
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 578-583 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The semiconducting compound CuGaxIn1 − xSe2 crystallizes in the chalcopyrite structure (space group I{\bar 4}2d, Z = 4). The X-ray powder data for x = 1, 0.75, 0.6, 0.5, 0.4, 0.25 and 0.0 have been collected and it is found that the lattice parameters a and c and their ratio c/a vary linearly with x. Thus the composition of any chalcopyrite in the pseudo-binary system CuGaSe2 and CuInSe2 can be obtained from the accurate lattice parameters. The crystallite size determined from the (112) plane is minimum for x = 0.50 ( ̃1000 Å) and away from x = 0.50 it increases. A value of u = 0.240 (5) has been established for fixing the Se-atom positions in the CuGa0.5In0.5Se2 solid solution. The JCPDS Diffraction File No. for CuInSe2 is 40-1487 and for CuGa0.5In0.5Se2 is 40-1488.
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    Applied crystallography online 22 (1989), S. 641-641 
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    Applied crystallography online 22 (1989), S. 642-642 
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  • 51
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    Applied crystallography online 22 (1989), S. 1-8 
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    Topics: Geosciences , Physics
    Notes: The method of crystallographic refinement using molecular dynamics [Brünger, Kuriyan & Karplus (1987). Science, 235, 458–460] has been implemented to work with the GROMOS simulation package. It has been tested by applying it to the structure of phospholipase A2. The structure of this molecule had previously been refined at high resolution with conventional methods. The new method successfully refined the initial multi-isomorphous replacement structure, removing most of the errors, without any manual intervention. All the refinement was performed at 300 K. The use of lower-resolution data allows greater conformational transitions to occur whereas the inclusion of high-resolution data results in a more accurate structure.
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  • 52
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    Applied crystallography online 22 (1989), S. 19-22 
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    Topics: Geosciences , Physics
    Notes: Drawings of molecular and solid-state structures generated by the computer program SCHAKAL88 are presented. Automatic atom labelling and some of the graphical techniques used for shading of line and raster drawings are briefly discussed.
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  • 53
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    Applied crystallography online 22 (1989), S. 26-34 
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    Notes: In paper I [Groma, Ungár & Wilkens (1988). J. Appl. Cryst. 21, 47–53] a theory was developed to interpret the asymmetric X-ray line broadening of plastically deformed crystals. It was shown that the dislocation structure can be described by five distinct parameters, namely the dislocation density, the mean quadratic spatial fluctuation of the dislocation density, the effective outer cut-off radius, the dipole polarization and the spatial fluctuation of the dipole polarization of the dislocation structure. In this paper a procedure is developed to evaluate these parameters from the Fourier transform of the line profiles. The theory and this procedure are tested by applying it to the asymmetric line profiles of tensile-deformed Cu single crystals orientated for ideal multiple slip. The asymmetry of these profiles is assigned to the dipole polarization of the dislocation cell structure and is directly correlated to residual long-range internal stresses. It is shown that the data can be interpreted in terms of the quasi-composite model of the dislocation cell structure developed earlier for the same material.
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  • 54
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    Applied crystallography online 22 (1989), S. 53-60 
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    Topics: Geosciences , Physics
    Notes: An automatic procedure has been developed for indexing reflections on oscillation photographs produced by crystals with very large unit cells (cell dimensions larger than about 100 Å). The procedure works in a similar fashion to the auto-indexing used in four-circle diffractometry. Features include ab initio cell parameter and orientation matrix determination, reduced cell calculation and transformation of the reduced cell to one with higher symmetry.
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  • 55
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    Applied crystallography online 22 (1989), S. 70-70 
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    Topics: Geosciences , Physics
    Notes: Owing to a printer's error, the key reference of the paper by Gilmore & Brown [J. Appl. Cryst. (1988), 21, 571–572] was omitted. The reference is here given in full.
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  • 56
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    Applied crystallography online 22 (1989), S. 72-74 
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    Topics: Geosciences , Physics
    Notes: Small-angle X-ray diffraction patterns from the anterior byssus retractor muscles of Mytilus edulis contracting tonically in response to stimulation with acetylcholine were recorded in a 30 s exposure with synchrotron radiation and a high-sensitivity X-ray area detector called an imaging plate. The 190 Å layer line from the thin filaments increased in intensity with increase in tonic tension up to 6 x 104 kg m−2. Above this value, the layer-line intensity remained almost constant and comparable to that for a contracting skeletal muscle, indicating that the same structural changes of the thin filaments occur in both muscles.
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    Applied crystallography online 22 (1989), S. 76-77 
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  • 58
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    Applied crystallography online 22 (1989), S. 84-86 
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    Notes: The use of asymmetric Bragg reflection offers the possibility of separating wavelength bands belonging to a fundamental wavelength and its higher harmonics from each other. This is shown in an example calculated for X-rays. Especially for well collimated synchrotron radiation the subsequent use of symmetric and asymmetric reflections in a double-crystal arrangement results in different large shifts of the reflected peaks. This kind of synchrotron monochromator offers two important improvements with respect to other similar monochromator systems: (a) it is tunable to the harmonics of a fundamental wavelength in a large range, e.g. from 0.4 to 2.7 Å; and (b) it works harmonic free for each wavelength band on top of the Darwin curve.
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  • 59
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    Applied crystallography online 22 (1989), S. 110-114 
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    Notes: A variable-size `box' method is described which optimizes the precision with which integrated intensities of neutron Bragg reflections are measured with an Anger camera. The consequent improvements in the least-squares-fitted crystallographic structural parameters and R-factors in test experiments on MnF2 and Cr3Si are substantial.
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  • 60
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    Applied crystallography online 22 (1989), S. 119-122 
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    Notes: High-pressure X-ray diffraction studies have been performed on powder samples of β-Ti3O5 (C2/m) for pressures up to 38.6 GPa using synchrotron radiation and a diamond-anvil cell. The compressibility is highly anisotropic. Thus, the compression Δl/l0 for the maximum pressure investigated is 5.4, 0.8 and 6.7% for the unit-cell axis directions a, b and c, respectively. The anisotropy is reasonable, considering the crystal structure. The bulk modulus B0, determined from the Murnaghan equation, is 173(10) GPa and B′0 is 7(1).
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  • 61
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    Applied crystallography online 22 (1989), S. 150-154 
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    Notes: A new equation involving an absorption coefficient is presented for calculating the thickness of a layer of a crystalline specimen deposited on a crystalline substrate. This new equation is particularly applicable to in situ X-ray diffraction studies of diffusion-limited kinetics; it is demonstrated that the practical difficulty of optimally partitioning count time between the peak of the substrate and peak of the layered specimen is overcome by making use of all available data in this single equation. This can result in more precise thickness determinations for intermediate specimen thicknesses than would be possible with either of the existing methods.
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  • 62
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    Applied crystallography online 22 (1989), S. 173-180 
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    Notes: Positional parameters (x, y, z) and anisotropic Debye–Waller factors B⊥ (normal to the xy plane) and B|| (parallel to the xy plane) have been determined for the Fe and Cl atoms in FeCl3 within the space group R{\bar 3} with a = 6.065, c = 17.42 Å. These are (0, 0, 1/3), BFe⊥ = 1.75 and BFe|| = 1.2 Å2 for the Fe atoms at 6(c) positions in the hexagonal-axis representation, and (0.358, 0, 0.078), BCl⊥ = 1.6 and BCl|| = 1.55 Å2 for the Cl atoms at 18(f) positions. In addition to the crystallographic parameters, the observed twinning is discussed using the possible variants of ABC and ACB stacking sequences, each of which has two variants with a 60° rotation of the chlorine lattice. One of the four twin variants is found to be strongly enhanced. The fit for these parameters yields a reliability factor R = \sum_{i} \parallel F^{i}_{\rm cal} \mid - \mid F^{i}_{\rm obs}\parallel / \sum_{i} \mid F^{i}_{\rm obs} \mid = 0.60.
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  • 63
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    Applied crystallography online 22 (1989), S. 184-185 
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    Notes: SWATAB is a Fortran IV computer program which helps in obtaining most of the required tables for crystal structure publication from the widely used SHELX76 program output. The strategy, installation, required local modifications, merits and limitations are discussed.
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  • 64
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    Applied crystallography online 22 (1989), S. 187-187 
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  • 65
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    Applied crystallography online 22 (1989), S. 201-204 
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    Notes: Multiple diffraction using parallel-beam synchrotron X-radiation is described. Data recorded on the Daresbury Synchrotron Radiation Source from a single-crystal of InSb are presented and compared with data recorded with the pseudo-Kossel technique. The wide-beam synchrotron technique has demonstrated for the first time the feasibility of the synchrotron radiation multiple-diffraction topographic technique. Potential applications for this technique in the characterization of low-dimensional structures are outlined.
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  • 66
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    Applied crystallography online 22 (1989), S. 189-200 
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    Notes: Backscatter Kikuchi diffraction has been applied to an investigation of a selection of nickel sulfide crystals. In the first instance the technique itself was investigated to see whether it could be used successfully to distinguish between the space groups P21/a{\bar 3} (Pa{\bar 3}) of pyrite and Pnnm of marcasite. Subsequently, it was used to investigate the structure of a thin epilayer which was observed to have grown on selected facets of a certain synthetic nickel pyrite crystal. The epilayer was shown to be rhombohedral with possible space groups R{\bar 3}2/m (R3m) and lattice parameters ar = 6.4 Å, αr = 36°. In an attempt to positively identify this structure, the technique was applied to a number of related compounds including the mineral millerite (NiS, R3m), α-NiS – a high temperature polymorph of millerite (P63/mmc and P63mc), and the layer compound NiI2 (R{\bar 3}m). It was concluded that the epilayer was most probably NiCl2 formed by reaction of the NiS2 crystal with chlorine contained in the carrier gas used during the chemical vapour deposition growth process.
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  • 67
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    Applied crystallography online 22 (1989), S. 222-230 
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    Notes: The wide-angle X-ray diffraction patterns of carbon fibres are strongly modulated by disorder in the stacking of carbon layers, preferred orientation and the measuring conditions. A method has been developed to characterize the crystallites in carbon fibres by applying the theory on the wide-angle X-ray diffraction of materials comprising. layer-type molecules, previously reported by the present authors [Shioya & Takaku (1988). Acta Cryst. A44, 150–157]. A set of pseudo-inverse functions which relate the characteristic values of the intensity distribution to the structural parameters has been proposed, and the structural parameters have been evaluated by iterative calculation of these pseudo-inverse functions and the intensity distribution. It is suggested that the interlayer spacing between carbon layers is distributed according to a skewed function having a longer tail at larger spacings.
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    Applied crystallography online 22 (1989), S. 256-260 
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    Notes: The Rietveld method has been modified to incorporate line broadening from strains, particle size and microtwins. It has been applied to TiFeD1.9. The structure was determined to be orthorhombic [a0 = 7.0426 (2), b0 = 6.2371 (2), c0 = 2.8315 (1) Å] in space group Cmmm, in agreement with recent studies. The material is heavily twinned on the (110) planes with an average distance between twin planes of 24 Å.
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  • 69
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    Applied crystallography online 22 (1989), S. 269-276 
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    Notes: Double-crystal X-ray diffraction rocking curves can be used to evaluate composition and thickness of epitaxic layers. In order to assess the limits of this technique, the 004 rocking curves of molecular-beam epitaxy- (MBE) grown coherent AlGaAs/GaAs epitaxic layers have been measured. The composition was calculated both by using theoretical values for the lattice parameters of the limiting compositions together with Vegard's law and also by using an epitaxic layer of AlAs as an in situ standard. The accuracy of this concentration measurement is evaluated by comparing it with an independent measurement of the composition. MBE-grown AlxGa1 − xAs (x = 0.3, 0.5, 0.7) epitaxic layers in the thickness range 0.2–6.0 μm were used to investigate the usefulness of the X-ray rocking-curve method for layer thickness measurement. The experimental rocking curves are compared with those generated from computer simulations based on X-ray dynamical scattering theory. In the thickness range 0.5–2.0 μm Bragg-geometry Pendellösung fringes are also observed. The layer thicknesses calculated from the integrated intensity ratios and the fringe spacings agree with layer thicknesses obtained from scanning electron microscope (SEM) sections. The applicability of this method to multiple layers is investigated using test structures.
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    Applied crystallography online 22 (1989), S. 287-293 
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    Notes: LATTICEPATCH is an interactive graphics program used to evaluate strategies for measuring X-ray diffraction data with area detectors. It is written in C and runs on the Silicon Graphics IRIS Series 3000 computers. It displays, at designated resolution, a sphere in reciprocal space and indicates the area(s) on its surface that both satisfy the Bragg condition and are projected onto the detector surface(s) during φ and ω rotations of the goniostat. The user can determine an efficient strategy for obtaining a unique set of data by changing interactively the goniostat settings. The orientation of the crystal may be changed to accommodate the use of several crystals. Symmetry operations may be invoked to produce equivalent scans and the reciprocal-space representation may be rotated about the x, y and z axes of the screen. The relevant calculations are discussed, the program is described and the development of strategies in several cases using LATTICEPATCH is examined.
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    Applied crystallography online 22 (1989), S. 298-298 
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  • 72
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    Notes: Two time-of-flight powder diffractometers have operated at the Intense Pulsed Neutron Source (IPNS) since August 1981. These instruments use dedicated microcomputers to focus time-of-flight events so that data from different detectors can be summed into a single histogram. Thus, large multidetector arrays can be employed at any scattering angle from 12 to 157°. This design permits data to be collected over a uniquely wide range of d spacings while maintaining high resolution and count rates. The performance of the two instruments is evaluated by analyzing data from a standard Al2O3 sample by the Rietveld method. These instruments provide the capability for moderate- to high-resolution measurements with the duration of a typical run being a few hours.
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    Notes: Bovine serum albumin (BSA) was dissolved in a mixture of deuterated glycerol and heavy water. The clusters formed by the 3300 proton spins in each BSA molecule were dynamically polarized up to P = 40%. Spin-contrast variation in small-angle neutron scattering was studied at several target polarizations. Zero contrast, and hence minimum polarized neutron small-angle scattering, is expected at PH = 60% from extrapolation of present data. The three basic scattering functions of spin-contrast variation look very similar because the shape of the BSA molecule and its proton distribution are congruent. Neutron small-angle scattering of BSA is similar to X-ray small-angle scattering at room temperature, indicating no deterioration of the molecular structure of BSA on solidification.
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    Applied crystallography online 22 (1989), S. 363-371 
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    Notes: Methods which determine the number and disorder of lattice planes in a crystal from the Fourier cosine coefficients of the intensity profile of an X-ray reflection use only the low harmonics and require that the coefficients be normalized so that the zero harmonic is unity. Experimentally, the profiles can only be recorded over a smaller range of scattering angle than required by the theory, and it is necessary to subtract background, which is likely to be estimated with considerable error, before determining the coefficients. It is shown that with polymer fibres this causes serious errors in the normalization, and in the values of those low harmonics used in the size and disorder determination, and prevents reliable values being obtained. Methods which avoid normalization and use only high harmonics are needed. It is shown that disorder may be obtained in such a way, but not size, for which low-order normalized coefficients are essential. A method of extrapolation is described and tested which enables the accurate high harmonics to be used to improve the estimates of the low ones. Whilst this will yield more reliable values of crystal size than are obtainable from existing methods, the accuracy depends entirely on the validity of the extrapolation, which cannot be tested in many cases of interest.
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    Applied crystallography online 22 (1989), S. 387-389 
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    Notes: RAD is an interactive computer program for radial distribution analysis of X-ray diffraction data from amorphous materials. RAD has been written in Fortran 77 and runs on IBM PC/XT/AT or compatible computers.
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    Applied crystallography online 22 (1989), S. 389-393 
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    Notes: SIR88 is an integrated package of computer programs for the solution of crystal structures. The package is based on the estimation of one- and two-phase structure seminvariants and three- and four-phase structure invariants according to the theory of representations [Giacovazzo (1977). Acta Cryst. A33, 933–944; (1980). Acta Cryst. A36, 362–372]. The program works in all the space groups and in most cases it is able to provide the correct solution without user intervention. Some prior information like the availability of a partial structure or of pseudotranslational symmetry is easily exploited to obtain the structure solution.
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    Applied crystallography online 22 (1989), S. 398-398 
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    Applied crystallography online 22 (1989), S. 406-409 
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    Notes: A method of subsurface layer structure investigation based on the measurement of diffraction as well as reflection in grazing-incidence geometry is presented. A specific feature of this method is that the incident beam is nearly parallel to the surface and suffers diffraction along with reflection, which leads to a significant decrease of the radiation penetration depth. As a result, the above methods turn out to be rather sensitive to the structure of thin (1–100 nm) crystal layers near the surface. The effect of an amorphous layer on the angular dependence of grazing X-ray scattering is studied. The theoretical part of the work is based on the well known Parratt formulae for the reflection coefficient and also on the modified two-wave diffraction theory.
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    Applied crystallography online 22 (1989), S. 455-459 
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    Notes: The indexing strategy of our sixteen-year-old powder-pattern indexing program has recently been revised. Several enhancements lead to an increased reliability and much shorter computing times in indexing difficult patterns, especially monoclinic.
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    Applied crystallography online 22 (1989), S. 465-469 
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    Notes: The crystallite orientation distributions of three magnetically aligned samples: YBa2Cu3O6 aligned in the tetragonal phase followed by oxidation for orthorhombic conversion, orthorhombic YBa2Cu3O7, and orthorhombic HoBa2Cu3O7, were studied by neutron pole-figure measurements. Each had a fiber texture with the c axis parallel to the applied-magnetic field direction. The orientation distributions could be described quite satisfactorily with Lorentzian or March distribution functions. The sample aligned in the tetragonal phase had distinctly better alignment than that aligned in the orthorhombic phase, with FWHMs of 19.3 (3) and 37.8 (7)°, respectively. The contour lines of the pole figures showed irregularities owing to the presence of coarse grains in the samples.
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    Applied crystallography online 22 (1989), S. 498-499 
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    Notes: The method of adding colour to an otherwise monochrome image to enhance interpretability is very common. However, many of the commonly used colour tables tend to obscure rather than to enhance fine gradations of intensity, and are not suitable for images with exceptionally large dynamic ranges. A colour table has been set up to achieve fine resolution over a wide dynamic range.
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    Applied crystallography online 22 (1989), S. 500-506 
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    Notes: A new program complex for macromolecular refinement is described. The kernel of the complex is the program FROG2 to refine proteins, RNA and other biopolymers. Its high-speed operation is due to the fast differentiation and the fast Fourier transform algorithms it uses. A model can be described along four levels: generalized parameters, atomic parameters, density distribution and diffraction parameters. The functional to be minimized is set by special reference files which make it easy to modify. The functional consists of many criteria; some of them, such as the phase criterion, are new; others, the density criterion and intermolecular interaction, are encountered, though not very often; and the rest of them are familiar, like R-factor, bond-length or bond-angle restraints. A model may be a mixture of individual atoms and rigid groups, each group including an arbitrary number of atoms. The complex has a routine to organize atoms into rigid groups for the most common situations. The FROG2 program does not in practice restrict model size or space group. However, it takes account of symmetry, which gives another reduction of computing time. The program does not require special effort to adapt it to any memory. It can easily be extended by new criteria, atomic types, and more effective algorithms for calculating electron density or Fourier transform may be included. Finally, program blocks may be used in other programs, e.g. those for phase refinement.
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    Applied crystallography online 22 (1989), S. 519-522 
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    Notes: Procedures for an independent characterization of lyotropic nematics by X-ray diffraction (XD) are presented. Nc (cylindrical micelles) and Nd (discotic micelles) can be distinguished on the basis of surface orientation alone by a method of sample scanning through the X-ray beam. The sign of the diamagnetic anisotropy susceptibility can also be independently obtained. The differences between optical and XD information for such a characterization are discussed.
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    Applied crystallography online 22 (1989), S. 556-558 
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    Notes: There is a simple way to apply non-crystallographic symmetry during the course of crystallographic coordinate refinement or structure determination by molecular replacement. A phase set is generated from the molecular coordinates which is invariant with respect to the non-crystallographic symmetry.
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    Applied crystallography online 22 (1989), S. 569-571 
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    Notes: Simplified representations of components of nucleic acids have been designed and implemented as programs integrated with other software that draws schematic diagrams of proteins. Examples illustrating the structures of oligonucleotides, tRNA and a protein–nucleic acid complex indicate the utility of these representations for making intelligible illustrations of complex structures containing nucleic acids.
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    Applied crystallography online 22 (1989), S. 562-568 
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    Notes: A small position-sensitive 3He gas detector has been developed for diffraction studies using short-wavelength neutrons. It covers 32 × 32 pixels with a 2 mm resolution, which in the present set up corresponds to 0.25°, and the efficiency is 75% at a wavelength of 0.8 Å. The detector has been used for standard data collection, as well as for studies of twinned crystals and measurements involving parasitic reflections. In all cases it has improved the mode and speed of the measurement, with gain factors compared with single detectors which range from more than two in standard measurements to several hundred for the study of details of the Bragg peak(s). The computation time in data analysis and the storage of the data are no major limitations, partly due to the smallness of the data array, and partly due to efficient packing routines.
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    Applied crystallography online 22 (1989), S. 592-600 
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    Notes: Rod-shaped scattering, referred to as crystal truncation rod (CTR) scattering in X-ray diffraction, can also be observed in optical diffraction patterns obtained from the surface profile image of high-resolution electron micrographs. The characteristics of the CTR scattering are shown to be in agreement with those observed by X-ray scattering. With this technique, information about the lattice relaxation of the image of surfaces or interface boundaries observed in the electron microscope (EM) can be easily obtained and the lattice spacing of a GaAs crystal is shown to be shrunk at the interface boundary between the (001) surface and the amorphous oxide layer. This is precisely opposite to the effect observed for an Si (001) wafer surface. Several effects of surface modulation on CTR scattering are demonstrated using an optical diffractometer and masks of the f.c.c. lattice.
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    Applied crystallography online 22 (1989), S. 627-629 
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    Notes: An algorithm to improve the computation time of packing calculations for macromolecules is presented. This is achieved by reducing the three-dimensional search to a small set of two-dimensional searches.
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    Applied crystallography online 22 (1989), S. 633-639 
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    Notes: CRYST is a three-dimensional computer graphics program to help the understanding of crystallographic procedures. The three-dimensional image of a crystal structure is displayed, together with the arrangement of the symmetry elements in the unit cell. The symmetry-related atoms can be generated successively on a graphics screen by designating symmetry elements with a pen and tablet. Changes in morphology of a growing crystal may also be drawn by computer. Several applications of the system are described.
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    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 40-44 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    Acta crystallographica 45 (1989), S. 49-51 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 109-111 
    ISSN: 1600-5759
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 134-136 
    ISSN: 1600-5759
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    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 178-180 
    ISSN: 1600-5759
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    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 185-187 
    ISSN: 1600-5759
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    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 191-194 
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    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 204-206 
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    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 208-210 
    ISSN: 1600-5759
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    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 215-218 
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    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 21-23 
    ISSN: 1600-5759
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