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  • International Union of Crystallography (IUCr)
  • 2010-2014  (32)
  • 1975-1979  (6,726)
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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
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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
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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 12 (1979), S. 628-628 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: An interactive program using a graphic display device for the analysis of small-angle scattering has been developed. It includes the curve fitting of experimental data to theoretical results calculated through a triaxial body approximation.
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  • 34
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 634-635 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A rapidly converging radial distribution least-squares program (RADILS) is available for the analysis of X-ray, neutron and electron diffraction data from liquid and amorphous materials. The program automatically generates a radial distribution function, G(r), essentially free from termination effects and determines the empirical background scale and shape, absolute scale factor, bulk density and coordination numbers, disorder parameters and interatomic distances for the first few highly ordered distances in the sample.
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  • 35
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 629-634 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A computer program which can identify the crystalline component phases of a mixture from its X-ray diffraction pattern is described. The program uses the data base of powder diffraction patterns maintained by the Joint Committee on Powder Diffraction Standards. The `reverse searching' technique employed permits the identification of each component and provides an estimate of confidence in the identification. Errors in measured spacings and intensities are tolerated by the program. The interactive search-match system is available for general use via a networked timeshared computer.
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  • 36
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 25-26 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A simple modification of the jig proposed by the IUCr Commission on Crystallographic Apparatus for the measurement of polarization ratios for X-rays allowing the full rotation of the detector arm permits cancellation of the first-order errors by averaging pairs of measurements differing by 180° around the rotation axis of the detector arm. The plot of Imeas as a function of cos2 Φ, where Φ is the angle between the detector arm and one of the principal directions of polarization in the beam gives a reliable value of the polarization ratio K. The experimental results are: Mo Kα 0.969 ± 3, 0.970 ± 3; Cu Kα 0.908 ± 5, 0.897 ± 5 for a 0.42° and a 0.60° FWHM graphite monochromator respectively.
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  • 37
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 34-38 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: X-ray diffraction data for three aqueous solutions of MgCl2 were analyzed. It is shown that in a very concentrated solution the structure and correlation functions can be reproduced almost completely by using a nearest-neighbor model of ionic hydration, whereas in the more dilute solutions a certain number of interactions between the hydrated cation and external water molecules must also be considered. The mean coordination geometry for the close hydration was found to be octahedral both for cation and anion with mean cation–water distances (2.10–2.12 Å) and mean anion–water distances (3.11–3.14 Å) in accordance with results found in other cases.
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  • 38
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 27-33 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Model calculation based on parallel cylindrical fibrils with a distribution of radii are used to derive fibrillar radii obtained from the transverse intensity profile of the small-angle X-ray scattering (SAXS) peaks. The results are expressed in terms of moments of the distribution function of the radii. The traverse integral breadth of the peak leads to ({\bar R^4}/{\bar R^3}), the initial slope gives ({\bar R^6}/{\bar R^4})1/2, the asymptotic slope in the transverse wings yields {\bar R^2} or ({\bar R^4}/{\bar R^2})1/2 and the analysis of the characteristic function gives ({\bar R^2}/{\bar R^1}). The first two methods are applied to the SAXS patterns of well oriented samples of nylon 6, for which it is found that a positively skewed distribution of fibrillar radii. The relation between these analyses of uniaxially oriented systems and other SAXS and wide-angle diffraction methods is considered.
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  • 39
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 39-41 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A computation method is presented which allows a rapid indexing of any unknown spot pattern obtained by back-reflection or transmission Laue methods. The Cartesian coordinates of n spots are measured in an orthonormal frame referred to the photographic film. Two spots 1 and 2 separated by a wide angular distance αm are carefully chosen. Their indices are assumed to be less than 5. The set (E) of all the pairs of planes (h1k1l1) and (h2k2l2) making an angle α close to αm is then computed. Since the pair of reflecting planes related to spots 1 and 2 belongs to (E), each computed pair of planes is tried, in order to determine the orientation of the crystal and to check whether the coordinates of the (n−2) other spots can be matched to dense planes of indices less than 8. If the uncertainty of the measurements is high or if n is too low, this method gives the possible orientations for the crystal. Plane indices less than 8 have been identified in cubic, tetragonal and orthorhombic crystals.
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  • 40
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 49-53 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Measurements of lattice parameters and birefringence of PbTiO3 single crystals are described as a function of temperature. The anomalous rise in birefringence with temperature is interpreted in terms of lattice strain and dielectric polarization.
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  • 41
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 116-118 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A process giving the limits of a peak measured by the step-scan method is described. This calculation is based on the research of the minimum of a convolution of the intensity. It is found on theoretical peaks (Gaussian and Lorentzian) that this algorithm gives less unbiased estimation of the integrated intensity than the one described previously by Lehmann & Larsen [Acta Cryst. (1974), A30, 580–584].
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  • 42
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 138-138 
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  • 43
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 138-138 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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  • 44
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: In all organisms the multi-subunit enzyme DNA-dependent RNA polymerase catalyses the first basic step in gene expression, the transcription of DNA into RNA. The neutron small-angle scattering effects were studied in the Guinier region by applying the contrast-matching technique. Isotopic labelling was realised by culturing fully deuterated E. coli cells in a heavy-water medium containing deuterated substrates. One or two completely deuterated components (subunits) of polymerase holoenzyme (composition formula α2ββ′σ, molecular weight 497000) were recombined with the remaining natural (`hydrogenated') subunits for these neutron measurements. Measurements are presented of radii of gyration R, overall shapes, and pair distances d, of three components (subunits α2β,β′) in RNA polymerase of E. coli. The subunits β′, β and α2 are obviously rather elongated in situ and exhibit (as scattering-equivalent prolate ellipsoids) axial ratios of about 7:1 up to 9:1. The intersubunit centre of gravity distances were analysed to be 7.3 ± 0.8 nm for β−β′, 8.2 ± 1.2 nm for α2−β′ and 7.0 ± 1.7 nm for α2−β.
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  • 45
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 186-191 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: It is demonstrated experimentally that the well known spin-selective deflection of neutrons transmitted through a static magnetic field region with triangular geometric boundaries combined with the high angular resolution of a non-dispersive double-crystal arrangement can be used to polarize a thermal neutron beam to a degree close to unity at reasonably low laboratory fields of 1.0 to 1.5 T.
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  • 46
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 12 (1979), S. 192-200 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A long-wavelength neutron scattering facility at the SAFARI-1 reactor is described. Neutrons of wavelength between 5 and 15 Å can be selected. Features of the facility are the use of microwave guides as neutron conductors, flexible guide-pipe configuration and automatic sequential sample changing. Examples are given of measurements on radiation-induced voids in copper, aluminium, Al-0.4%Si and Al-0.1%In after neutron irradiation and magnetic scattering in US and in 80US-10UC-10UC2.
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  • 47
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    Applied crystallography online 12 (1979), S. 201-204 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The development is critical in recording X-ray topographs since it takes a long time and determines the final quality of the pictures. It is shown that, in most cases, it is possible to decrease both exposure time and development time and still obtain pictures of good quality. Standard conditions of development should be used to achieve higher resolution only. This new standard may be of great use with the modern high-power sources.
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  • 48
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    Applied crystallography online 12 (1979), S. 205-208 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The doping method in quantitative X-ray diffraction phase analysis is described. The method involves the addition to the investigated system of known amounts of the components, the weight fractions of which are to be simultaneously determined. The weight fraction of a component is related to the intensities diffracted by that component and by any non-added component, before and after doping. The method can also be applied to systems containing unidentified components by analysing for only those components of interest, as well as for amorphous-content determination.
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  • 49
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    Applied crystallography online 12 (1979), S. 209-220 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A method for quantitative determination of local curvature in elastically bent perfect crystals is described. The method is based on X-ray intensity measurements, and a comparison of experimentally determined values with those derived from diffraction theory gives satisfactory agreement. The method was applied to determine the strain gradient and strain concentration in the vicinity of the notch of an elastically bent crystal. The experimental results were compared with those derived from a similar model based on continuum mechanics. Possible applications of the X-ray method are discussed to obtain experimental solutions to strain analyses which, when approached by continuum mechanics, pose formidable mathematical obstacles.
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  • 50
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    Applied crystallography online 12 (1979), S. 221-224 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A film-type X-ray high-temperature (up to about 2250 K) powder camera using the Guinier focusing principle in transmission is described. Use is made of a germanium monochromator. The powder specimen is spread without adhesive on a horizontal supporting film of refractory material, and rotates about a vertical axis. The support is surrounded by a cylindrical furnace of thin tantalum sheet enclosed in a chamber which can be evacuated or filled with an inert gas. The X-radiation enters and leaves the chamber through beryllium windows. The film holder is situated outside the chamber. The sample temperature is measured by thermocouples and optical pyrometry. Problems due to the coating by evaporated material of the silica glass window used to observe the specimen are obviated by the use of a transparent shield which can be rotated to give fresh surfaces when needed.
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  • 51
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    Applied crystallography online 12 (1979), S. 240-241 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: β-LiAlO2 was reindexed on the basis of an orthorhombic crystal system with cell dimensions: a = 5.283 (3), b = 6.306 (4) and c = 4.908 (2) Å.
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  • 52
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    Applied crystallography online 12 (1979), S. 225-238 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A method is described for the processing of X-ray diffraction data collected on an Arndt–Wonacott rotation camera particularly suitable for crystals with very large unit cells. Since often only single exposures can be obtained before the radiation has damaged such crystals, it is essential to select accurately those reflections which have fully penetrated the sphere of reflection. This requires not only a careful refinement of the crystal setting orientation but also a good knowledge of the mosaic spread plus beam divergence. The necessary parameters can be determined by convoluting the theoretically predicted diffraction pattern against the observed film in search of the maximum similarity. Films taken with the crystal misset by as much as 1° can readily be processed with rotational corrections reproducible to better than 0.01°. The many very weak intensities found in data derived from crystals with very large unit cells can be better measured by using a least-squares fit to a previously determined profile rather than by the usual integration process. Systematic variation of the profile across the surface of the film can be readily accommodated.
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  • 53
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    Applied crystallography online 12 (1979), S. 241-242 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Cs2[Pd(CN)4].H2O and Cs2[Ni(CN)4].H2O were found to be isotypic with the known hexagonal Pt compound which shows an unusual helical chain of six [Pt(CN)4]2− groups in the unit cell, space group P61 or P65. The crystal data are a = 9.559 (2) and c = 19.308 (4) Å, Dm = 2.87 (4), Dx = 2.912 Mg m−3 for the Ni compound, and a = 9.704 (2), c = 19.388 (4) Å, Dm = 3.12 (4), Dx = 3.115 Mg m−3 for the Pd compound. X-ray powder data are given.
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    Applied crystallography online 12 (1979), S. 261-261 
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  • 55
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    Applied crystallography online 12 (1979), S. 262-262 
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  • 56
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    Applied crystallography online 12 (1979), S. 267-274 
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    Topics: Geosciences , Physics
    Notes: The filter theory allows one to compare the efficiencies of smoothing procedures widely used in the field of small-angle X-ray scattering. This method is demonstrated for polynomial fitting and modified frequency filtering. Optimized and objective smoothing parameters are determined for both procedures through the knowledge of variance reduction factors, transfer functions of the filters, the largest value of the spatial frequencies of the scattering curve and the distortions caused by the smoothing procedures. The comparison of the efficiency of polynomial fitting and frequency filtering clearly shows the superiority of the latter; therefore, this method has to be preferred.
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  • 57
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    Applied crystallography online 12 (1979), S. 263-266 
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    Topics: Geosciences , Physics
    Notes: A structural refinement of ammonium hydrogen tartrate, C4H9NO6, has been completed from data obtained on an Enraf–Nonius CAD-4 X-ray diffractometer equipped with a Si(Li) solid-state detector. The refinement has given comparable results with those found in the literature. A comparative study of a select number of weak reflections obtained from this study and from the results of an analysis using a conventional scintillation system indicates that the peak-to-background ratio is better for intensity data collected on an X-ray diffractometer using a Si(Li) solid-state detector system. An important application of a Si(Li) energy-dispersive system is X-ray fluorescence analysis which can be performed on the same single-crystal employed in X-ray diffraction data collection. Qualitative determinations and quantiative data on relative percentages of metal constituents have been obtained from single crystals of Lu(OH)3 and Mn3[Co(CN)6]2.12H2O in less than two hours.
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    Applied crystallography online 12 (1979), S. 275-278 
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    Topics: Geosciences , Physics
    Notes: A recent experiment on neutron diffraction by microscopically curved silicon crystals has shown the existence of the Fankuchen effect, which is a space condensation of neutrons occurring for this kind of crystal. This paper reports an experimental analysis of neutron focusing in the Fankuchen effect for curved crystals. The focusing effect in a symmetrical geometry was also investigated for comparison. The results are discussed and a conclusion is derived concerning a gain in neutron current density for the Fankuchen geometry, particularly interesting for neutron diffractometry of small biological crystals.
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    Applied crystallography online 12 (1979), S. 279-286 
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    Topics: Geosciences , Physics
    Notes: The design, operating principles and constructional details of a goniometer for use in ultra-high-resolution objective-lens pole-pieces are described. Image-matching of experimental and computer-simulated high-resolution electron micrographs is used to demonstrate an instrumental resolution of 1.6 Å, point-to-point.
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    Applied crystallography online 12 (1979), S. 425-425 
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    Applied crystallography online 12 (1979), S. 425-426 
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    Applied crystallography online 12 (1979), S. 427-428 
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    Applied crystallography online 12 (1979), S. 426-427 
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    Applied crystallography online 12 (1979), S. 428-428 
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    Applied crystallography online 12 (1979), S. 428-428 
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    Applied crystallography online 12 (1979), S. 429-431 
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    Notes: X-ray, neutron and electron diffraction experiments have revealed the existence of internally ordered Guinier–Preston zones in Al-(8 to 15 at.%)Mg alloys; diffuse satellites oriented along (100) directions are observed near Bragg peaks and give rise to modulated contrasts by TEM. A small-angle neutron scattering experiment has been carried out on single crystals and a model is proposed for the interpretation of the observed pattern. The existence of concentration modulations is related to alignments of spherical GP zones along (100) directions.
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    Applied crystallography online 12 (1979), S. 436-441 
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    Notes: The analytical algebraic method developed for the selection of active slip systems in the case of glide on {110} (111) systems [Royer, Mohr & Tavard, J. Appl. Cryst. (1978). 11, 35–39] is extended to (111) pencil glide. This approach leads to an algebraic determination of all amounts of glide and corresponding slip plane orientations in both cases of effective slip on three or four systems. Numerical applications have led to a reduction of computer time by a factor of 10−3 with respect to previous investigations.
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    Applied crystallography online 12 (1979), S. 476-480 
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    Notes: The early stages of the decomposition process in the ternary Cu-9 wt.% Ni-6 wt.% Sn alloy have been studied by transmission electron microscopy. The supersaturated solid solution was found to decompose through the spinodal mechanism into periodic and aligned regions which are Sn-rich and Sn-lean. It was also found that in addition to this clustering reaction, an ordering reaction also progressed with the ageing treatment to produce a metastable phase with the DO22 (Al3Ti type) structure. However, on prolonged ageing, a discontinuous reaction started at the grain boundaries and consumed the matrix leaving behind colonies of a pearlitic product composed of the equilibrium α (A1 structure) and the γ (DO3 structure) phases. This paper discusses the mechanism of formation of the DO22 phase in the alloy.
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    Applied crystallography online 12 (1979), S. 481-482 
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    Notes: Synthetic crystals of tachyhydrite are trigonal, diffraction aspect R**, with hexagonal parameters a = 10.136 (1), c = 17.318 (2) Å, U = 1540.9 (3) Å3, Z = 3, Dc = 1.673 Mg m−3. Indexed powder data are given.
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    Applied crystallography online 12 (1979), S. 473-475 
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    Notes: Ten alloys have been investigated in the composition range from V3Si to Cr3Si across the ternary equilibrium diagram using X-ray diffraction, neutron diffraction, superconducting transition temperature and magnetic susceptibility measurements. Contrary to the results of previous workers it is shown that a two-phase region is present in the mid-composition ranges. The vanadium-rich (VCr)3Si solid solution shows superconducting properties. A magnetic structure appears at low temperatures in certain alloys in the chromium-rich (CrV)3Si solid solution range.
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    Applied crystallography online 12 (1979), S. 482-483 
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    Notes: X-ray powder data of tetrakis(ethyl isocyanide)platinum(II) tetracyanoplatinate(II), [Pt(CNC2H5)4] [Pt(CN)4], C12H20N4Pt2+. C4N4Pt2−, are given. A tetragonal unit-cell with lattice constants of a = 9.223 (30) and c = 3.339 (1) Å is suggested.
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    Applied crystallography online 12 (1979), S. 483-485 
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    Topics: Geosciences , Physics
    Notes: A computer program POWLS for refinement of crystal structures and magnetic structures from X-ray or neutron diffraction powder diagrams is reported. The program uses integrated intensities as the observed quantities. It is highly flexible.
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    Applied crystallography online 12 (1979), S. 485-486 
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    Notes: A set of Fortran programs for the refinement of crystal structures using the Rietveld profile analysis technique have been written or adapted for use on an interactive computer. Facilities include distance and angle calculations, Fourier calculations and Madelung site energy calculations as well as the main refinement option.
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    Applied crystallography online 12 (1979), S. 487-487 
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    Applied crystallography online 12 (1979), S. 487-487 
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    Applied crystallography online 12 (1979), S. 488-488 
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    Applied crystallography online 12 (1979), S. 488-488 
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    Applied crystallography online 12 (1979), S. 488-488 
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    Applied crystallography online 12 (1979), S. 511-516 
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    Notes: High-pressure time-of-flight neutron diffraction studies have been carried out on orthorhombic Ge2N2O to 25.4 × 108 Pa and by X-ray diffraction to 49 × 108 Pa. The zero-pressure axial compressibility coefficients are Ka = 33 (2), Kb = 41 (2), Kc = 28 (2), and volume Kv = 99 (5) × 10 −13 Pa−1. The changes in bond angles and bond lengths at pressures from 105 to 25.4 × 108 Pa have been measured. The structure of Ge2N2O consists of GeN3O tetrahedra linked along the a direction by Ge–O–Ge bonds and along the b and c directions by three coordinated Ge–N bonds. This structural framework adjusts to applied pressure by tetrahedra tilting in a cooperative fashion, the biggest change being observed in the Ge–O–Ge angle which decreases by 12.4°. The behavior of Ge2N2O is very similar to its isomorph Si2N2O, though the tetrahedra deform somewhat more for Ge2N2O. The pressure changes in the lattice parameters of Ge2N2O up to 8̃ × 108 Pa are very similar to those of Si2N2O up to 2̃4 × 108 Pa, supporting the contention that germanates behave as high-pressure models for silicates.
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    Applied crystallography online 12 (1979), S. 517-524 
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    Notes: A Monte Carlo model is developed to simulate the X-ray fluorescence process within a homogeneous multi-element mixture. Validation of the model is obtained through comparison of the model's predictions with experimental data for the iron–nickel–chromium system, for which the inter-element effects are severe. The results indicate that the Monte Carlo model is an excellent simulator and may be used in place of a set of standards to determine the influence coefficients for analysis of fluorescence data.
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    Applied crystallography online 12 (1979), S. 582-584 
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    Notes: The mass absorption factor μ*0j of an unknown sample can be determined by mixing of the sample with a substance for which the mass absorption coefficient μ*0K is known, and then measuring the intensity of the analytical lines of the mixture and the sample. The optimal concentration of a substance added to the unknown sample is determined by the conditions which will give a minimal analytical error. The optimal concentration is equal to 1/(1 + 2μ*0K/μ*0j) when mixing is effected with a sample containing the phase to be determined (method of addition) or with an internal standard and to 1/(1 + 0.5 μ*0K/μ*0j) when mixing is performed with a substance which does not contain the phase to be determined (dilution method).
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    Applied crystallography online 12 (1979), S. 570-581 
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    Notes: When collecting data using oscillation photography, it is necessary to distinguish between those reflections which have passed completely through the Ewald sphere (`full reflections') and those whose penetration is incomplete (`partial reflections'). Such differentiation requires an accurate knowledge of crystal setting parameters. This is particularly necessary if partial reflections are to be used when adjacent films do not originate from the same crystal. In general this is the case where diffracted intensities are weak, as in crystals of oligomeric proteins and viruses. Estimates of setting parameters can be obtained by comparing a partial reflection on one film with a full observation of the same reflection on the same or another film [Schutt, C. E. & Winkler, F. K. (1977). The Rotation Method in Crystallography, edited by U. W. Arndt & A. J. Wonacott, pp. 173–186. Amsterdam: North-Holland]. A measure of the observed degree of partiality, pobs, can thus be made and related to the calculated value, pcalc, derived from the crystal setting parameters. Least-squares minimization of E = Σω(pobs − pcalc)2 leads to the refinement of (1) the orientation of each crystal, (2) the crystal cell dimensions and (3) each crystal's effective mosaic spread. Examples of this technique are provided from the processing of high-resolution southern bean mosaic virus data.
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    Applied crystallography online 12 (1979), S. 585-588 
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    Notes: The radial distribution function [g(r)] of a liquid can be obtained from an integral transform of its X-ray scattering intensity I(μ). Experimentally, I(μ) can be measured over only a limited range, leading to termination errors in g(r). Using the strict positivity of g(r), an iterative method is proposed to reduce these errors. The negative portions of each successive distorted approximation of g(r) are replaced by the value zero and this function is used to generate I(μ) in the non-measured range. Computer calculations on a model function yield encouraging results. The method appears to have an advantage over current approaches as it does not require a knowledge of the hard-core diameter of the atoms. It is also expected to work in the case of molecular liquids where there are some difficulties in applying the current methods.
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    Applied crystallography online 12 (1979), S. 589-591 
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    Notes: An electron diffraction pattern of cotton cellulose recording over 70 reflections per quadrant out to the tenth layer line could be indexed on the basis of the Meyer & Misch [Helv. Chim. Acta (1937). 20, 232–244] model. The validity of the observations based on the reciprocal net a*c* when checked by constructing reciprocal net b*c* revealed that three reflections could not be indexed. No systematic absence of odd-order 0k0 reflections was noted. The cotton cellulose, therefore, does not fall into P21 space group.
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    Applied crystallography online 12 (1979), S. 617-618 
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    Notes: The ionic conductor N(CH3)4GeCl3 shows a phase transition at 424 K. The high-temperature modification is cubic with a = 6.552 (2)Å, space group Pm3m. At 293 K the compound is orthorhombic with unit-cell parameters a = 13.096 (2), b = 8.911 (1), c = 9.128 (2) Å, space group Pna21.
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    Applied crystallography online 12 (1979), S. 618-618 
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    Notes: The crystal structure determination of ethyl-4-acetoxy-5-methoxy-8-bromo-2-naphthoate has been undertaken with a view to finding out the molecular packing and the nature of the intermolecular bonding.
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    Applied crystallography online 12 (1979), S. 621-622 
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    Notes: The α form of iminodiacetic acid, HN(CH2COOH)2, C4H7NO4, is found to be orthorhombic, space group Pb21a. The lattice parameters of the unit cell with eight molecules are a0 = 14.172 (7), b0 = 14.977 (8) and c0 = 5.276 (3) Å. The crystals melt with decomposition at 520 (2) K. X-ray powder diffraction data are reported.
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    Applied crystallography online 12 (1979), S. 619-621 
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    Notes: The structure of room temperature PuGa has been determined. The material has a body-centered tetragonal lattice, space group I4mm (No. 107), Z = 8, a = 6.6408 ± 12, c = 8.0833 ± 20 Å, and a calculated density of 11.50 Mg m−3. Intensity data was obtained from a powder-pattern film taken with Cr Kα radiation, λ = 2.2909 Å. The structure, which deviates slightly from an ideal subcell, was refined by least-squares calculation to R1 = 0.079 using 39 observed reflections. Pu–Pu distances range from 3.08 to 3.40 Å, Pu–Ga distances from 3.07 to 3.26 Å, and Ga–Ga distances from 2.75 to 3.89 Å.
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    Applied crystallography online 12 (1979), S. 623-626 
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    Notes: Ca8[Al12O24](WO4)2, formerly believed to be cubic, is tetragonal. It forms a superstructure with the usual 9 Å unit cell of sodalites.
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    Applied crystallography online 12 (1979), S. 626-627 
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    Notes: The preliminary single-crystal data and powder pattern are given for a second polymorph of C.I. Pigment Red 1, C16H11N3O3. The powder pattern has been indexed using the single-crystal dimensions; the problems of multiple indexing have been reduced by comparison with single-crystal intensities.
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    Applied crystallography online 12 (1979), S. 636-638 
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    Notes: An interactive electron-image calculation system has been developed. The system contains all the necessary programs to model interactively a crystal structure and calculate and display the image on a graphics terminal.
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    Applied crystallography online 12 (1979), S. 638-639 
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    Applied crystallography online 12 (1979), S. 639-639 
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    Applied crystallography online 12 (1979), S. 639-640 
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    Applied crystallography online 12 (1979), S. 640-640 
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    Applied crystallography online 12 (1979), S. 640-641 
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    Applied crystallography online 12 (1979), S. 641-641 
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