issue contents

Journal logoJOURNAL OF
APPLIED
CRYSTALLOGRAPHY
ISSN: 1600-5767

February 2010 issue

Highlighted illustration

Cover illustration: PDB_REDO optimization of the oldest structure with experimental data in the PDB [155c; Timkovich & Dickerson (1976). J. Biol. Chem. 251, 4033-4046]. Front: final structure - warmer colours show greater atomic displacement. Back: final structure model with atomic trajectories in yellow. Courtesy of Joosten et al. [J. Appl. Cryst. (2009), 42, 376-384].

research papers


J. Appl. Cryst. (2010). 43, 1-7
doi: 10.1107/S0021889809044112
link to html
The capillary condensation and capillary emptying of water and perfluoropentane in ordered mesoporous SBA-15 silica is studied by in-situ small-angle neutron scattering (SANS). The SANS data can be perfectly described by a simple analytical model for spatially random pore filling (Laue scattering) for the entire range of pore-filling fractions.

J. Appl. Cryst. (2010). 43, 8-11
doi: 10.1107/S0021889809048675
link to html
The theory of small-angle scattering of a multiphase system, its relation to scattering contrast variation and the ability to extract the scattering pattern of a single phase are considered.

J. Appl. Cryst. (2010). 43, 12-16
doi: 10.1107/S0021889809048791
link to html
A novel theory is presented which allows the analytical description of small-angle scattering experiments on anisotropic shaped clusters of nanoparticles. Experimentally, silica-filled rubber which is deformed is used as an example.

J. Appl. Cryst. (2010). 43, 17-26
doi: 10.1107/S002188980904758X
link to html
The diffraction-line broadening exhibited by three different Pb3O4 phases was studied at ambient and elevated pressures. The broadening indicates strongly anisotropic microstrain, which was interpreted in terms of (local) stress variations in association with strongly anisotropic elastic properties.

J. Appl. Cryst. (2010). 43, 27-32
doi: 10.1107/S0021889809051577
link to html
A new method is proposed to improve structure modeling by taking into account the half-wavelength contribution (λ/2) to X-ray data measured on CCD and image-plate diffractometers.

J. Appl. Cryst. (2010). 43, 33-37
doi: 10.1107/S0021889809050936
link to html
The phase diagram of the Nd–Pt system from 35 to 85 at%Pt has been revised using X-ray diffraction and differential thermal analysis.

J. Appl. Cryst. (2010). 43, 38-41
doi: 10.1107/S0021889809047037
link to html
Extinction has been found on pole figures measured by neutron diffraction on highly textured high-purity copper. A possible mechanism responsible for the extinction is proposed.

J. Appl. Cryst. (2010). 43, 42-47
doi: 10.1107/S0021889809047748
link to html
This article defines optimal steric crowding around an apical water mol­ecule. The apical bond length shows sigmoidal dependence on distortion of the coordination polyhedron.

J. Appl. Cryst. (2010). 43, 48-52
doi: 10.1107/S0021889809050547
link to html
Lithium tantalate (LT) single-crystalline fibers with various growth conditions were obtained using the laser-heated pedestal growth (LHPG) method. To facilitate wave propagation with low loss, glass-clad LT fibers were fabricated by a co-drawing LHPG method for the first time.

J. Appl. Cryst. (2010). 43, 53-57
doi: 10.1107/S002188980904134X
link to html
A method is described for automated least-squares molecular overlay without a priori atomic correspondence or connectivity information. The method is applied to compare crystallographically distinct molecules in 18 941 single-component molecular crystal structures taken from the Cambridge Structural Database.

J. Appl. Cryst. (2010). 43, 58-63
doi: 10.1107/S0021889809051917
link to html
This report describes the application of organic solvent gels and aqueous hydrogels for crystallization of soluble and membrane proteins. The hydrogel is based on polyvinyl alcohol and the organic based gels are formed using polyethylene oxide, which is compatible with a variety of solvents. Diffracting crystals were obtained with both gel systems.

J. Appl. Cryst. (2010). 43, 64-69
doi: 10.1107/S0021889809046342
link to html
This paper describes a technique for collecting X-ray absorption fine structure from perfect crystals, free of large systematic errors.

J. Appl. Cryst. (2010). 43, 70-82
doi: 10.1107/S0021889809043234
link to html
EVAL15, a novel diffraction data integration method, predicts reflection profiles that are used to determine accurate intensities. It can solve a range of difficult diffraction problems, such as those related to overlap, Kα1/Kα2 peak splitting and satellite reflections.

J. Appl. Cryst. (2010). 43, 83-88
doi: 10.1107/S0021889809046548
link to html
In nuclear spectroscopy by crystal diffraction, Bayesian inference allows γ-ray photons and rocking angles detected in coincidence to be used to find the location of the diffraction peak without binning the recorded angles.

J. Appl. Cryst. (2010). 43, 89-100
doi: 10.1107/S0021889809050535
link to html
The phase-retrieving performance of the structure solution methods charge flipping and low-density elimination is investigated. The best strategies are discussed.

J. Appl. Cryst. (2010). 43, 101-109
doi: 10.1107/S0021889809043076
link to html
A novel procedure for the determination of the molecular weight of proteins in dilute solution from a single small-angle X-ray scattering curve measured on a relative scale is described.

J. Appl. Cryst. (2010). 43, 110-121
doi: 10.1107/S0021889809043271
link to html
A newly installed small/wide-angle X-ray scattering (SAXS/WAXS) instrument for structural characterization is described. The instrument performance is illustrated via a variety of measurements, including simultaneous SAXS/WAXS and grazing-incidence SAXS from the air–water interface.

J. Appl. Cryst. (2010). 43, 122-133
doi: 10.1107/S0021889809043957
link to html
The micropipe-induced birefringence of 6H silicon carbide is measured and quantitatively modelled, using the rotating polarizer method.

J. Appl. Cryst. (2010). 43, 134-139
doi: 10.1107/S0021889809045889
link to html
This work provides a new methodology for the analysis of misorientations in textured materials; its aim is also to shed some light on the development of recrystallization textures in hexagonal materials, which are still largely not understood.

J. Appl. Cryst. (2010). 43, 140-150
doi: 10.1107/S0021889809049851
link to html
Incommensurate satellite reflections modulating along the 〈110〉* directions have been observed in the electron diffraction patterns of single crystals of the relaxor ferroelectric Pb2ScTaO6 (PST). The satellites represent a weak frustrated antiferroelectric state in PST, termed the incommensurate antiferroelectric state.

J. Appl. Cryst. (2010). 43, 151-153
doi: 10.1107/S0021889809048006
link to html
A pseudo single crystal of sucrose (monoclinic, P21) was prepared and the origin of its twin orientation is discussed.

J. Appl. Cryst. (2010). 43, 154-162
doi: 10.1107/S0021889809050560
link to html
Urea doping leads to the enhancement of second-harmonic generation (SHG) efficiency in tristhioureazinc(II) sulfate (ZTS) single crystals, with a critical dependence on urea concentration. An interesting correlation between crystalline perfection and SHG efficiency has been revealed using high-resolution X-ray diffractometry and Kurtz powder techniques.

J. Appl. Cryst. (2010). 43, 163-167
doi: 10.1107/S0021889809047499
link to html
The crystal structures of two pharmaceutical compounds were solved from laboratory and high-resolution powder diffraction data collected at the ESRF Grenoble. The serious problems encountered during an ab initio crystal structure solution from powder data are described and discussed.

J. Appl. Cryst. (2010). 43, 168-175
doi: 10.1107/S0021889809052753
link to html
Large crystals of two siliceous zeolites have been grown and studied as a function of temperature using bifrefringence microscopy. In one case organic template is retained and the crystals show a reversible, ferroelastic phase transition on heating and cooling, but in another the bifrefringence indicates migration of organic template to the crystal edges upon heating.

short communications


J. Appl. Cryst. (2010). 43, 176-178
doi: 10.1107/S0021889809048109
link to html
A V-shaped channel-cut X-ray monochromator based on a graded Ge-rich GeSi single crystal with a total asymmetry factor of 21 is presented. It exhibited a peak intensity more than three times higher than that of a V-21 monochromator made of a pure Ge crystal.

computer programs


J. Appl. Cryst. (2010). 43, 179-180
doi: 10.1107/S0021889809049875
link to html
A close-contact penalty factor has been added to the GEST structure solution from powder diffraction data software to differentiate chemically unreasonable structure models from potentially correct models. It has proved an effective method to eliminate chemically unreasonable trial models.

J. Appl. Cryst. (2010). 43, 181-185
doi: 10.1107/S0021889809051929
link to html
A cross-platform program, ISAACS, has been developed to analyze the structural properties of three-dimensional structure models obtained using computer simulations (molecular dynamics, ab-initio molecular dynamics, reverse Monte Carlo, Monte Carlo etc.). A wide range of calculations can be performed, including radial distribution functions, simulation of neutron and X-ray diffraction, ring statistics, and spherical harmonics.

J. Appl. Cryst. (2010). 43, 186-190
doi: 10.1107/S0021889809045701
link to html
An expert system for macromolecular crystallography data reduction using existing software, xia2, is presented with examples of its application to a range of data sets.

J. Appl. Cryst. (2010). 43, 191-195
doi: 10.1107/S0021889809049267
link to html
A plug-in (EXTRAX) has been developed for ImageJ – a public domain Java-based program widely used for image processing and analysis in microscopy. This plug-in allows the extraction and measurement of intensities from electron diffraction spot patterns with a semi-automatic peak location based on a two-dimensional lattice given by the user.

J. Appl. Cryst. (2010). 43, 196-199
doi: 10.1107/S002188980903982X
link to html
A web-accessible resource has been created to study the interactions of various metal ions present in macromolecular structures.

J. Appl. Cryst. (2010). 43, 200-202
doi: 10.1107/S0021889809048626
link to html
An online web server coupled with a knowledgebase has been created to study the interactions of various ligand molecules with three-dimensional macromolecular structures.

J. Appl. Cryst. (2010). 43, 203-205
doi: 10.1107/S0021889809047050
link to html
This paper describes a computing server, SSMBS, which can locate and display the occurrences of user-defined biologically important sequence motifs (a maximum of five) present in a specific order in protein and nucleotide sequences.

laboratory notes


J. Appl. Cryst. (2010). 43, 206-210
doi: 10.1107/S0021889809049693
link to html
Safety considerations involving `icing-up' with solid air of the sample space of top-loading cryostat equipment are discussed, where uncontrolled de-icing may cause a flash-to-gas, leading to trapped volumes being placed under high pressure. Methods of prevention and resolution of freeze-ups are elaborated, and a case is made for using a helium leak detector as part of sample changing.

international union of crystallography


J. Appl. Cryst. (2010). 43, 211-215
doi: 10.1107/S0021889809047876

Follow J. Appl. Cryst.
Sign up for e-alerts
Follow J. Appl. Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds