forthcoming articles

The following articles are a selection of those recently accepted for publication in IUCr journals.

IUCrJ
Accepted 31 January 2019

Evaluation of the performance of classification algorithms for XFEL single-particle imaging data

X-ray free-electron lasers were used for single-particle imaging of 3D nanoscale structures. Through the extraction of single-particle diffraction patterns from the data, the performances of image-classification algorithms were evaluated and the final reconstruction results depended on the selection of dataset.

Accepted 31 January 2019

Ice formation and solvent nanoconfinement in protein crystals

Nanoconfinement dramatically modifies the behaviour of solvent within protein crystals, allowing biophysical measurements in the presence of liquid solvent at temperatures down to ~200 K. When internal ice forms it is stacking disordered, consistent with nucleation within deeply supercooled solvent, and ice does not form in solvent within ~5 Å of the protein surface.

Accepted 28 January 2019

Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition

The co-crystal structure of the metallopeptidase astacin with its specific protein inhibitor fetuin-B reveals a novel mechanism of inhibition.

Accepted 25 January 2019

Fixed-target serial oscillation crystallography at room temperature

The combination of oscillation data collection with fixed-target microchips for regular crystal dispersion is an efficient method for collecting serial crystallography data at synchrotrons. Background scatter from noncrystal substrates is especially minimized.

Accepted 22 January 2019

Time-resolved grazing-incidence pair distribution functions during deposition by radio-frequency magnetron sputtering


Accepted 9 January 2019

Local atomic structure of thin and ultrathin films via rapid high-energy X-ray total scattering at grazing incidence

The short- and long-range order of thin films with thicknesses down to 3 nm were studied by applying PDF analysis to data collected by surface high-energy X-ray diffraction at a time resolution on the scale of seconds.
Journal logoActa Crystallographica Section A
Acta Crystallographica
Section A
FOUNDATIONS AND ADVANCES

Accepted 24 January 2019

On Two Special Classes of Parallelohedra in E^6


Accepted 22 January 2019

Shape transform phasing of edgy nanocrystals

Reconstruction of an object from the averaged coherent diffracted intensity of finite crystals of that object with arbitrary lattice occupancies is possible. An algorithm capable of reconstructing both the so-called averaged shape transform and the object density at the same time is demonstrated.

Accepted 9 January 2019

Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies

The transferable aspherical pseudoatom data bank, UBDB2018, is extended with over 130 new atom types present in small and biological molecules of importance in biology and chemistry. UBDB2018 can be used to enhance the physical meaning of molecular electrostatic potentials twhich can be utilized in, amongst other fields, drug discovery studies.

Accepted 8 January 2019

Aperiodic Order: Volume 2, Crystallography and Almost Periodicity


Accepted 7 January 2019

Identification of the impurity phase in high-purity CeB6 by convergent-beam electron diffraction

The impurity phase in high-purity CeB6 is unequivocally identified by first determining its space group, using an iterative convergent-beam electron diffraction (CBED) approach, and following this with an atomic structure confirmation by quantitative convergent-beam electron diffraction (QCBED) and high-angle annular dark-field scanning transmission electron microscopy.

Accepted 4 January 2019

Bonding network and stability of clusters: the case study of Al13TM4 pseudo-tenfold surfaces


Accepted 3 January 2019

Full real-space analysis of a dodecagonal quasicrystal

Analysis of a dodecagonal quasicrystal based on 8100 vertices from atomically resolved scanning tunnelling microscopy has been carried out. A detailed frequency and orientational analysis is presented for the triangle–square–rhomb tiling of a BaTiO3-derived quasicrystal.

Accepted 26 December 2018

Group-theoretical analysis of 1:3 A-site-ordered perovskite formation

A group-theoretical analysis of 1:3 A-site-ordered perovskite structures is reported.

Accepted 24 December 2018

Aspects of the topology of actinide atom substructures in crystal structures and the concept of antiliquid

Consideration of the maximum space-filling principle and the short-range (local) and long-range (translational) order using Voronoi–Dirichlet polyhedra reveals the most probable number of neighboring atoms and the concept of antiliquid.

Accepted 10 December 2018

Principles of weakly ordered domains in intermetallics: the cooperative effects of atomic packing and electronics in Fe2Al5

The Fe2Al5 structure is remarkable among intermetallic phases for its channels of weakly ordered Al atoms. This article traces the origins of these channels to the cooperative effects of soft atomic motions dictated by chemical pressure quadrupoles and preferred electron concentrations.

more ...
Journal logoActa Crystallographica Section B
Acta Crystallographica
Section B
STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS

Accepted 10 February 2019

Crystal structure and XANES investigation of petzite, Ag3AuTe2

Single-crystal XRD and XANES investigation of the mineral petzite is reported.

Accepted 5 February 2019

Accurate geometrical restraints for WC base pairs

Revised geometrical parameters are proposed for the Watson-Crick pairs of nucleobases, for use as restraints in modeling and refinement of nucleic acids structures. Accurate values of these parameters were derived (and compared) from small-molecule CSD structures, from super accurate ultrahigh-resolution nucleic acid structures in the PDB, and from quantum mechanical calculations. The effect of base-pairing on the molecular geometry of the nucleobases was also investigated.

Accepted 4 February 2019

Developing new SrI2 and β-D-fructo­pyran­ose-based metal–organic frameworks with NLO properties

This article describes novel strontium iodide–fructose-based metal–organic frameworks (MOFs), with NLO [nonlinear optical] properties, with a high potential for theranostic applications in cancer radiotherapy.

Accepted 31 January 2019

Accepted 25 January 2019

Quantum pressure focusing in solids: a reconstruction from experimental electron density

The indicator of quantum pressure focusing displays the inner-crystal regions where the electronic pressure is concentrated or depleted due to the quantum kinetic, exchange and correlation effects. It reveals the chemical bond features in crystals, using orbital-free formalism of the density functional theory in combination with experimental electron density.

Accepted 22 January 2019

The formation of the salt and neutral molecule cocrystal from equimolar solution of heli­amine and bi­cyclo­[2.2.1]hept-5-ene-endo-2,3-di­carb­oxy­lic acid

The unusual cocrystal of salt and neutral molecule was formed from the equimolar solution of 6,7-di­meth­oxy-1,2,3,4-tetra­hydro­iso­quinoline (heli­amine) and bi­cyclo­[2.2.1]hept-5-ene-endo-2,3-di­carb­oxy­lic acid due to peculiarities of crystal packing formation.

Accepted 22 January 2019

Thermal, spectroscopic and structural analysis of a thermosalient phase transformation in ta­pentadol hydro­chloride

A first-order phase transformation in tapentadol hydrochloride, taking place at ca. 318 (1) K (on heating) and 300 (1) K (on cooling) is described, and the changes in crystal structure relating the high-temperature and low-temperature forms are analyzed. The crystals present an ostensible thermosalient behaviour during the transformation, explainable through some abrupt unit-cell changes taking place.

Accepted 19 January 2019

Taxifolin tubes: crystal engineering and characteristics

Microtubes of taxifolin were synthesized by crystal engineering. They were characterized using physicochemical, microscopic, spectral and computational methods of analysis.

Accepted 18 January 2019

Using powder XRD and pair distribution function to determine anisotropic atomic displacement parameters of orthorhombic tridymite and tetragonal cristobalite

Anisotropic atomic displacement parameters of orthorhombic tridymite and tetragonal cristobalite can be determined accurately using the combined methods of powder XRD and pair distribution function analysis.

Accepted 9 January 2019

Acid–ammonium heterodimer and N(ammonium)–H⋯N(pyridine) synthon preference in the salts [→three salts]? of nicotinic acid with (1R,2R)-1,2-di­phenyl­ethyl­enedi­amine


more ...
Journal logoActa Crystallographica Section C
Acta Crystallographica
Section C
STRUCTURAL CHEMISTRY

Accepted 14 February 2019

Isolation and structure of an 18-membered macrocycle containing two diselenide linkages and its precursor

The structures of an 18-membered aza­macrocycle containing two disselenide linkages and its precusor are reported.

Accepted 31 January 2019

Synthesis, crystal structures and characterizations of three new copper(II) complexes including anti-inflammatory diclofenac

We report herein the structural and spectral properties of newly synthesized dimeric and monomeric copper(II) complexes including the anti-inflammatory diclofenac, namely {[Cu2(μ-dicl)4(CH3OH)2], [Cu(dicl)2(vim)2] and [Cu(dicl)2(im)2] (dicl is diclofenac, vim is 1-vinyl­imidazole and im is imidazole)}. In the complexes, different coordination modes of the dicl ligands were revealed by single-crystal X-ray diffraction analyses.

Accepted 21 January 2019

Inter­play between hydrogen and halogen bonding in the functionalization of the C=C bond in chalcone

Cooperative action of hydrogen and halogen bonding in the reaction of 3-(3,5-di-tert-butyl-4-hy­droxy­phen­yl)-1-phenyl­prop-2-en-1-one with HCl or HBr allows the isolation of the haloetherification products 3-(3-tert-butyl-5-halo-4-hy­droxy­phen­yl)-2-halo-3-alk­oxy-1-phenyl­propan-1-ones. Both inter­molecular hydrogen- and halogen-bond-supported active species were detected by ESI–MS analysis in solution.
Journal logoActa Crystallographica Section D
Acta Crystallographica
Section D
STRUCTURAL BIOLOGY

Accepted 12 February 2019

The third structural switch in the molecule of archaeal translation initiation factor 2 and its possible role in initiation of GTP hydrolysis and removal of aIF2 from the ribosome

The structure of aIF2γ in complex with GTPCP without Mg2+ ions in crystallization solution is determined and the new information about the role of Mg2+ ions in the function of aIF2ing is provided. The new functional region (switch 3) of the aIF2γ is discovered.

Accepted 4 February 2019

Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95

Crystal structures of the third PDZ domain of the neuronal postsynaptic density protein 95 lacking the third α-helix and protein variants D332P and D332G show conformational plasticity.

Accepted 30 January 2019

Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data

We have developed a method to combine quantum mechanical calculations and joint crystallographic refinement against X-ray and neutron data. Applications to structures of the galectin-3 C–lactose complex and lytic polysaccharide monooxygenase show that it can improve the geometry for water molecules, deuterium atoms and hydrogen bonds, as well as determine protonation states of key residues.

Accepted 16 January 2019

X-ray structure of an inactive zymogen clostripain-like protease from Parabacteroides distasonis

Cysteine proteases are among the most prominent hydrolytic enzymes produced by human distal gut commensal bacteria. Here, the first inactive zymogen structure of a clostripain-like C11 protease family member is reported from the bacterium P. distasonis.

Accepted 14 January 2019

Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L-pyroglutamate recognition


Accepted 4 January 2019

In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity

The paper describes the structure solution of human IBA57; to our knowledge, this is the only structure present in the Protein Data Bank which has been solved in-house by remote SAD phasing in space group P1 using only one crystal.

Accepted 3 January 2019

Engineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein di­sulfide isomerase ScsC from Proteus mirabilis


Accepted 28 December 2018

The atypical thiol–di­sulfide exchange protein α-DsbA2 from Wolbachia pipientis is a homotrimeric di­sulfide isomerase


Accepted 19 December 2018

Strategies for sample delivery for femtosecond crystallography

Strategies for sample delivery of macromolecular crystals at X-ray free-electron lasers are reviewed, covering injection methods, fixed-target approaches and hybrid methods.

Accepted 17 December 2018

Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a

The solution of a structure of human Rab27a suffering from severe anisotropy and translational noncrystallographic symmetry was aided by identifying diffraction measurements with low information content.

more ...
Journal logoActa Crystallographica Section E
Acta Crystallographica
Section E
CRYSTALLOGRAPHIC COMMUNICATIONS

Accepted 12 February 2019

Crystal structure of potassium [4-amino-5-(benzo[d]thia­zol-2-yl)-6-(methyl­sulfan­yl)pyrimidin-2-yl](phenyl­sulfon­yl)aza­nide di­methyl­formamide monosolvate hemihydrate

The title compound, the potassium salt of a benzo­thia­zol(methyl­sulfan­yl)pyriminidine, was obtained in a reaction designed to deliver a neutral 2-pyrimidylbenzo­thia­zole. It crystallized with two independent mol­ecular units in the asymmetric unit.

Accepted 2 January 2019

Synthesis, crystal structure, spectroscopic features and Hirshfeld surfaces of 2-methyl-3-[(2-methyl­phen­yl)carbamo­yl]phenyl acetate

2-Methyl-3-[(2-methyl­phen­yl)carbamo­yl]phenyl acetate was synthesized, characterized by IR spectroscopy, and its crystal structure was determined from single-crystal data. In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds. The two independent mol­ecules in the asymmetric unit adopt different conformations.
Journal logoActa Crystallographica Section F
Acta Crystallographica
Section F
STRUCTURAL BIOLOGY COMMUNICATIONS

Accepted 13 February 2019

Crystal structure of Cydia pomonella granulovirus PTP-2

The crystal structure of the betabaculovirus Cydia pomonella granulovirus protein phosphatase PTP-2 has been determined at 1.65 Å resolution. The structure shows that the molecule has a typical protein phosphatase fold with a unique β-sheet extension at the C-terminus.

Accepted 10 February 2019

Expression, purification and crystallization of Pseudomonas aeruginosa esterase PA2949, a bacterial homologue of human membrane esterase ABHD6

Homologous expression of a membrane-bound esterase PA2949 from P. aeruginosa PA01 and purification of detergent solubilized enzyme resulted in stable PA2949 protein which crystalized. Obtained crystals diffracting to a resolution of 2.74 Å were used for X-ray analysis.

Accepted 31 January 2019

Perdeuteration, large crystal growth and neutron data collection of Leishmania mexicana triose-phosphate isomerase variant E65Q

We describe the perdeuteration, large crystal growth and neutron diffraction data collection of Leishmania mexicana triose-phosphate isomerase variant E65Q.

Accepted 30 January 2019

Putative polysaccharide de­acetylase Ba0331: cloning, expression, crystallization and structure determination

The crystal structure of Ba0331, a putative polysaccharide deacetylase from Bacillus anthracis, was determined in the present study. The structure is comprised of two domains: a fibronectin type 3-like domain and a NodB catalytic domain.

Accepted 30 January 2019

The structure of lipopolysaccharide transport protein B (LptB) from Burkholderia pseudomallei

The structure of a lipopolysaccharide transport protein B (LptB) is reported. Comparisons with LptB from different bacterial species reveal that the dimeric assembly is independent of interaction with the rest of the transport machinery and significant sequence and structural conservation occurs where LptB interacts with its physiological partners.

Accepted 30 January 2019

Crystal structure of a putative peptide-binding protein AppA from Clostridium difficile

CdOppA and CdAppA are putative extracellular peptide binding proteins serving cognate ABC transporters in Clostridium difficile. Here with purified proteins we have found no evidence for (i) peptide binding to either protein in thermofluor experiments or (ii) the presence of peptides in the crystal structure of CdAppA. Further sequence analysis suggests that CdOppA is a nickel transporter protein and CdAppA may be involved in the transport of a restricted set of peptides.

Accepted 25 January 2019

BacMam production and crystal structure of nonglycosylated apo human furin at 1.89 Å resolution

The production of nonglycosylated human furin ectodomain via the BacMam expression system is reported. The protein is equally active compared with the glycosylated protein and is readily crystallized, and X-ray diffraction was used to solve a high-resolution structure.

Accepted 22 January 2019

Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase

The structure of a complex of M. tuberculosis decaprenyl diphosphate synthase with geranyl S-thiodiphosphate and isopentenyl S-thiodiphosphate was refined to 1.55 Å resolution. It not only shows the magnesium-coordinated configuration for catalysis but also suggests a pathway for product translocation as well as a direction for inhibitor design.

Accepted 22 January 2019

The structure of an iron-containing alcohol de­hydrogenase from a hyperthermophilic archaeon in two chemical states

The structure of a homodimeric, iron-containing alcohol dehydrogenase from a thermophile that utilizes NADP as its coenzyme was solved in three crystal forms. In two crystals one subunit of the asymmetric unit was occupied by NADP and the other was not, while in the third crystal no NADP or iron was present. The coenzyme is encapsulated in a tunnel that penetrates through the molecule, and the iron is totally sequestered.

Accepted 16 January 2019

Neutron and X-ray analysis of the Fenna–Matthews–Olson photosynthetic antenna complex from Prosthecochloris aestuarii

Large crystals of the Fenna–Matthews–Olson protein from P. aestuarii were grown in a new H3 space group that permitted room-temperature neutron diffraction data collection to 2.2 Å resolution.

more ...
Journal logoJournal of Applied Crystallography Journal of Applied
Crystallography

Accepted 30 January 2019

Characterization and application of Bragg edge transmission imaging for strain measurement and crystallographic analysis on the IMAT beamline

Characterization of Bragg edge transmission imaging on the new IMAT beamline at the ISIS pulsed neutron source is performed, and application of the technique is demonstrated. Bragg edge transmission is capable of producing accurate strain maps with high spatial resolution, and spatially resolved texture information, non-destructively.

Accepted 22 January 2019

Aqua­rium: an automatic data-processing and experiment information management system for biological macromolecular crystallography beamlines

Aqua­rium is an automatic data processing and experiment information management system for synchrotron radiation source MX beamlines. Aqua­rium is designed to automatically process datasets from data reduction to model building, and results presentation. Users can monitor and inspect the data processing results from the Aqua­rium website.

Accepted 21 January 2019

Understanding of stress and its correlation with microstructure near layer continuous limit in nano-scaled multilayer

Evolution of residual stress and its correlation with microstructure are investigated systematically in nano-scaled periodic W/B4C X-ray multilayers (MLs) as a function of individual layer thicknesses in ultra-thin limit (~0.4–2 nm). It is observed that the physical properties of materials, interfacial morphology and residual stress in film undergo a significant modification as the layer thickness varies from continuous to quasi-discontinuous regime, and are explained using a model of mechanism of film growth.

Accepted 21 January 2019

Anomalous Neutron Scattering "Halo" Observed in Highly Oriented Pyrolytic Graphite

An unexpected ring in the scattering pattern of highly oriented pyrolytic graphite (HOPG) was observed, which arises from the unique structural and dynamic features of HOPG. A possible interpretation by multiple scattering including elastic and inelastic processes is proposed.

Accepted 20 January 2019

Facile synthesis of novel antimony selenide nanocrystals with hierarchical architecture by physical vapor deposition technique


Accepted 20 January 2019

A new method of calculating interatomic spacing: the equal-ratio method

A new method of calculating interatomic spacing has been proposed.And the new method does not request any auxiliary illustration.

Accepted 18 January 2019

Free-film small-angle neutron scattering: a novel container-free in situ sample environment with minimized H/D exchange

A free-film sample environment for neutron scattering, particularly useful for in situ small-angle neutron scattering, is presented, providing a sample area of up to 7 × 20 mm and an average thickness of 500 µm. The instrumental background is reduced by 37% compared with standard Hellma cells, and a helium jacketing of the entire setup provides a minimized H/D exchange with the humidity from air.

Accepted 18 January 2019

A direct approach to estimate the anisotropy of protein structures from small-angle X-ray scattering

In this work, a Guinier-like approximation to directly estimate the anisotropy of molecules in solution from their small-angle X-ray scattering intensity around the origin is developed. This approach provides deeper insight into a molecule's structure than the traditional Guinier RG estimation and can be used in ab initio reconstruction methods to provide better initialization strategies.

Accepted 16 January 2019

An electrochemical cell for operando bench-top X-ray diffraction

An X-ray transparent electrochemical cell with dense glassy carbon windows (Sigradur-G) for operando bench-top X-ray diffraction in reflection geometry is demonstrated.
Journal logoJournal of Synchrotron Radiation Journal of
Synchrotron Radiation

Accepted 12 February 2019

Arrival timing diagnostics at a soft X-ray free-electron laser beamline of SACLA BL1

Arrival timing diagnostics between a soft X-ray free-electron laser and synchronized optical laser pulses was performed at SACLA BL1.

Accepted 31 January 2019

Fluorescence intensity monitors as intensity and beam-position diagnostics for X-ray free-electron lasers

A fluorescence intensity monitor has been developed for the non-invasive, pulse-by-pulse normalization of LCLS-II experiments. The linearity, noise and position sensitivity of the detectors have been characterized.

Accepted 29 January 2019

Optical performance and radiation stability of polymer X-ray refractive nano-lenses

Full-field X-ray microscopy with a resolution of 100 nm, achieved by polymer compound 3D refractive nano-lenses, is demonstrated. This article also dicusses issues related to lens aberrations, astigmatism and radiation stability, and thus ways of improving the lens further are considered.

Accepted 28 January 2019

The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source

A description of the Macromolecular Femtosecond Crystallography instrument at the Linac Coherent Light Source is given. Scientific capabilities are highlighted, performance parameters are presented along with some commissioning results.

Accepted 28 January 2019

Multiple-beamline operation of SACLA

The parallel operation of three free-electron laser (FEL) beamlines was first conducted using the SPring-8 Ångstrom Compact free-electron LAser, to offer more opportunities for advanced studies using X-ray FELs.


Accepted 18 January 2019

A versatile liquid-jet setup for the European XFEL

A versatile liquid-jet injection system for serial femtosecond crystallography at the SPB/SFX instrument of the European XFEL is presented. The system comprises a load-lock nozzle rod changer, chamber-in-chamber differential pumping, liquid handling systems and two microscopes for sample imaging and diagnostics.

Accepted 17 January 2019

An experimental platform using high-power, high-intensity optical lasers with the hard X-ray free-electron laser at SACLA


Accepted 14 January 2019

M-BLANK: a program for the fitting of X-ray fluorescence spectra

Elemental maps are compared from the fitting of X-ray fluorescence data from an X-ray microprobe using the common approach of correcting by a per-pixel baseline and this article's approach of using a blank. Using X-ray fluorescence data of yeast and glial cells, it is shown that per-pixel baselines can result in significant, systematic errors in quantitation and that significantly improved data can be obtained by using a blank spectrum.

Accepted 28 December 2018

Standing wave approach in the theory of X-ray magnetic reflectivity

An extension to the exact X-ray resonant magnetic reflectivity (XRMR) theory has been developed; advantages of analyzing rotated polarization (higher sensitivity to the depth profiles of magnetization and magnetic element depth distribution) in XRMR experiments are shown.

more ...
Journal logoIUCrData
IUCrData

Accepted 11 February 2019

Chiral crystal of (Z)-1-benzoyl-5-benzyl­idene-2-hy­droxy-4-oxo-4,5-di­hydro-1H-pyrrole-3-carbo­nitrile

The title compound crystallizes in space group P212121. The phenyl rings have a twisted conformation.

Accepted 10 February 2019

2-[3-(4-Chloro­phen­yl)-5-(4-fluoro­phen­yl)-4,5-di­hydro-1H-pyrazol-1-yl]-8H-indeno­[1,2-d]thia­zole

In the crystal, inversion-related pairs of mol­ecules are linked by weak C—H⋯N inter­actions, forming dimers. These dimers inter­act through π–π contacts between the thia­zolyl units [centroid-to-centroid distance = 3.826 (1) Å], forming chains along [010].

Accepted 10 February 2019

3-[5-Methyl-1-(4-methyl­phen­yl)-1H-1,2,3-triazol-4-yl]-1-phenyl-1H-pyrazole-4-carbaldehyde

The asymmetric unit consists of two independent mol­ecules. In the crystal, the two independent mol­ecules form dimers linked by four C—H⋯O hydrogen bonds with each O atom accepting two such links.


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