forthcoming articles

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

IUCrJ
Accepted 29 May 2020

A Self-Supervised Workflow for Particle Picking in Cryo-EM

A self-supervised workflow uses a 2D class average to progressively train a convolutional neural network for automated particle picking in Cryo-EM.

Accepted 22 May 2020

Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism

Through interaction studies, the crystal structure of human DHTKD1 allows insight into a mitochondrial megacomplex in lysine catabolism. This creates the starting framework for developing DHTKD1 modulators to probe the intricate mitochondrial energy metabolism..

Accepted 20 May 2020

1.8 Å resolution structure of β-galactosidase with a 200 kV CRYO ARM electron microscope


Accepted 14 May 2020

Induced DNA bending by unique dimerization of HigA antitoxin


Accepted 4 May 2020

Assessing JEOL CryoARM300 for high-throughput automated single-particle cryo-EM in a multiuser environment

This paper presents a detailed assessment of the performance of the CryoARM300 electron microscope in a multiuser cryo-EM facility setting. It is shown that the microscope can be used for reliable automated data collection. The strengths and weaknesses of the hardware are discussed.

Accepted 3 May 2020

Structural basis of self-assembling in the lipid-binding domain of mycobacterial polar growth factor Wag31

The crystal structure of the N-terminal membrane anchoring domain of mycobacterial DivIVA/Wag31 reveals a filament-compatible `dimer-of-dimer' assembly state. The result suggests that, in addition to lipid binding, the N-terminal Wag31 can participate in self-assembling to form filamentous structures.

Accepted 29 April 2020

Bond-length distributions for ions bonded to oxygen: results for the transition metals and qu­antification of the factors underlying bond-length variation in inorganic solids

Bond-length distributions are examined for transition metals bonded to O2−. Causal mechanisms underlying bond-length variation in inorganic solids are resolved, and the extent to which these mechanisms individually result in bond-length variation is quantified for transition metals with anomalous bond-length distributions.

Accepted 29 April 2020

Paired refinement under the control of PAIREF

Application of the PAIREF program providing automation of paired refinement is demonstrated on seven data sets. The results prove that the inclusion of high-resolution data beyond the conventional criteria can lead to more accurate structure models.
Journal logoActa Crystallographica Section A
Acta Crystallographica
Section A
FOUNDATIONS AND ADVANCES

Accepted 26 May 2020

Multiplicity-weighted Euler's formula for symmetrically arranged space-filling polyhedra

For many tested cases of identical space-filling polyhedra, such as the space-group-specific asymmetric units or Dirichlet domains, the numbers of their faces (Fn), edges (En) and vertices (Vn), in each case normalized by division by the multiplicity of their (potentially special) symmetry position, fulfill a modified Euler's formula Fn-En+Vn=1.

Accepted 16 April 2020

Theoretical study of the properties of X-ray diffraction moiré fringes. III. Theoretical simulation of previous experimental moiré images

Using a recently developed moiré-fringe theory of X-ray diffraction, computer simulations of previous experimental moiré images are presented, for an experimental verification of the moiré-fringe theory and for a theoretical explanation of the peculiar experimental moiré images.
Journal logoActa Crystallographica Section B
Acta Crystallographica
Section B
STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS

Accepted 27 May 2020

Polyoxometalate clusters in minerals: review and complexity analysis

The article reviews current progress in the investigations of polyoxometalate clusters in minerals.

Accepted 20 May 2020

Low temperature martensite relaxation in Co-Ni-Ga shape memory alloy monocrystal revealed using in situ cooling transmission electron microscopy and low rate calorimetry

Co49Ni21Ga30 magnetic shape memory monocrystal was studied using in situ imaging and low temperature calorimetry. Both methods confirmed the occurrence of local reconstruction of the crystal lattice at temperatures below 190 K.

Accepted 8 May 2020

Crystal forms and phase transformation of 1,5-pentanedi­amine-terephthalate: a bio-based nylon 5T monomer

Two hydrates of PDA-TPA crystal structures are determined and analysed, and crystal form (I) shows favourable stability. The phase transition between forms (I) and (II) depends strongly on the temperature and water activity, and the larger the value of water activity is, the higher is the transition temperature.

Accepted 5 May 2020

Variations of quantum electronic pressure under the external compression in crystals with halogen bonds assembled in Cl3, Br3, I3-synthons

Changes in quantum electronic pressure in crystals under external compression reveal spatial areas of relatively higher compressibility. The halogen bonds assembled in Hal3-synthons create the `stiff framework' in hexahalo­benzene crystals.

Accepted 20 April 2020

New insights about the structural properties of κ-(BEDT-TTF)2Ag2(CN)3 spin liquid

The first accurate study of the room-temperature and 100 K structures of one of the first organic spin liquids, κ-(BEDT-TTF)2Ag2(CN)3, is presented.
Journal logoActa Crystallographica Section C
Acta Crystallographica
Section C
STRUCTURAL CHEMISTRY
Journal logoActa Crystallographica Section D
Acta Crystallographica
Section D
STRUCTURAL BIOLOGY

Accepted 4 June 2020

Macromolecular crystallography beamlines at the Canadian Light Source: building on success

Describes the current capabilities and future upgrade plans of the beamlines supporting structural biology at the Canadian Light Source.

Accepted 1 June 2020

Two particle-picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER

Two approaches for the selection of filaments from cryo-EM micrographs are described.

Accepted 20 May 2020

A new modulated crystal structure of the ANS complex of the St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell

When crystallized in complex with the fluorescent dye 8-anilinonaphthalene-1-sulfonate (ANS) in the presence of melatonin, Hyp-1, a pathogenesis-related class 10 protein from Hypericum perforatum, produced tetartohedrally twinned C2 crystals with commensurate structure modulation, which was interpreted as a ninefold expansion of the unit cell in the c direction. The asymmetric unit of this supercell contains 36 protein molecules (differently populated by 156 ANS ligands) arranged into columns by a combination of ninefold translational noncrystallographic symmetry and pseudotetragonal rotational NCS.

Accepted 15 May 2020

Targeting the innate immune receptor TLR8 using small-molecule agents

The innate immune receptor TLR8 can be positively or negatively regulated by small chemical ligands. Structural views of agonist-bound and antagonist-bound forms have revealed the mechanisms underlying agonism and antagonism.

Accepted 11 May 2020

Making a difference in multi-data-set crystallography: simple and deterministic data-scaling/selection methods

Fast and deterministic methods, based on multi-dimensional scaling and weighted ΔCC1/2, to reject non-isomorphous data sets in multi-data-set crystallography are described, and their successful application to several difficult projects where phasing is based on weak anomalous signal is reported.
Journal logoActa Crystallographica Section E
Acta Crystallographica
Section E
CRYSTALLOGRAPHIC COMMUNICATIONS

Accepted 4 June 2020

Crystal structure and Hirshfeld surface analysis of 4-{2,2-di­chloro-1-[(E)-(4-chloro­phen­yl)diazen­yl]ethen­yl}-N,N-di­methyl­aniline

The asymmetric unit of the title compound comprises three independent mol­ecules of similar geometry. The crystal structure is stabilized by inter­molecular C—H⋯N and C—H⋯Cl hydrogen bonds in addition to C—Cl⋯π inter­actions.

Accepted 4 June 2020

Two N-{[4-(3-aryl-4-sydnonyl­idene­amino)-5-sulfan­ylidene-1H-1,2,4-triazol-3-yl]meth­yl}benzamides as disordered ethanol monosolvates

In each of the title newly synthesized and closely related N-{[4-(3-aryl-4-sydnonyl­idene­amino)-5-sulfanyl­idene-1H-1,2,4-triazol-3-yl]meth­yl}benzamides, which crystallized as ethanol monosolvates, the independent components are linked by hydrogen bonds to form centrosymmetric four-mol­ecule aggregates.

Accepted 3 June 2020

Methyl 3-[(1-benzyl-4-phenyl-1H-1,2,3-triazol-5-yl)formamido]­propano­ate: crystal structure, Hirshfeld surface analysis and computational chemistry

The title compound is constructed about a tri-substituted 1,2,3-triazole ring, with the substituent at the C atom flanked by the C and N atoms being a substituted amide group, and with the adjacent C and N atoms bearing phenyl and benzyl groups, respectively. In the crystal, pairwise amide-N—H⋯O(carbon­yl) hydrogen bonds give rise to a centrosymmetric dimer.

Accepted 1 June 2020

Reductive cleavage of N,N′-di-tert-butyl­carbodi­imide generates tert-butyl­cyanamide ligands, (Me3CNCN), that bind potassium both end-on and side-on in the same single crystal

The crystal structure is reported of a single crystal containing potassium salts of two different tert-butyl­cyanamide anions that co-crystallized with one equivalent of 1,3-di-tert-butyl urea.

Accepted 29 May 2020

Crystal structure and Hirshfeld surface analysis of one-dimensional copper(II) coordination polymer incorporating succinate and tetra­methyl­ethylene­diamine ligands

The title compound, {[Cu(succ)(tmeda)]·4H2O}n, consists of one-dimensional polymeric chains in which the central metal atom is coordinated in a distorted square-planar geometry by one oxygen atom each from two succ ligands and two TMEDA ligand nitro­gen atoms.

Accepted 1 April 2020

Comparison of two MnIVMnIV-bis-μ-oxo complexes {[MnIV(N4(6-Me-DPEN))]2(μ-O)2}2+ and {[MnIV(N4(6-Me-DPPN))]2(μ-O)2}2+

The addition of tert-butyl hydro­peroxide (tBuOOH) to two MnII complexes, differing by a small synthetic alteration from an ethyl to a propyl linker in the ligand scaffold, results in the formation of the high-valent bis-oxo complexes {[MnIV(N4(6-Me-DPEN))]2(μ-O)2}2+ (1) and {[MnIV(N4(6-Me-DPPN))]2(μ-O)2}2+ (2).
Journal logoActa Crystallographica Section F
Acta Crystallographica
Section F
STRUCTURAL BIOLOGY COMMUNICATIONS
Journal logoJournal of Applied Crystallography Journal of Applied
Crystallography

Accepted 26 May 2020

In Situ Temperature Profile Measurements with High Energy X-rays as a Probe of Optical Floating Zone Crystal Growth Environment

A new synchrotron-compatible furnace for simulating the environment inside an optical floating zone furnace is described. It is shown that temperature profiles within heated rods can be determined from in situ synchrotron diffraction data, and that these measured profiles can be reproduced with a four-component heat transfer model.

Accepted 22 May 2020

Accepted 9 May 2020

Defining the hematite topotaxial crystal growth in magnetite–hematite phase transformation

Determination of a growth model of hematite crystals derived from magnetite–hematite phase transformation from a new orientation condition.

Accepted 8 May 2020

A new approach to phason disorder for a decagonal quasicrystal: the moment series expansion of the tiling distribution function for AlCuRh

This paper reports the application of the moment series expansion of the characteristic function of the distribution associated with the geometric part of the structure factor to model phason disorder in the structure refinement of the decagonal quasicrystal AlCuRh. The major result is that combining a new approach to phasons with the standard Gaussian Debye–Waller formula gives better refinement results and a finer atomistic model of quasicrystals, based on the decagonal AlCuRh system.

Accepted 7 May 2020

Chirok: a post-refinement tool to analyse absolute structure

Chirok is a new tool for a post-refinement analysis of absolute structures. It is based on the fit of a statistical distribution of Parsons quotients with various peak functions.

Accepted 2 May 2020

Dark-field electron holography as a recording of crystal diffraction in real space: a comparative study with high-resolution X-ray diffraction for strain analysis of MOSFETs

A detailed theoretical and experimental comparison of dark-field electron holography (DFEH) and high-resolution X-ray diffraction (HRXRD) is performed. Both techniques are applied to measure elastic strain in an array of transistors and the role of the geometric phase is emphasized.

Accepted 1 May 2020

In situ monitoring of hydrothermal reactions by X-ray diffraction with Bragg–Brentano geometry

A feasibility study is carried out of an autoclave chamber for in situ X-ray diffraction experiments under hydrothermal conditions. Quartz dissolution and tobermorite formation are monitored on conventional laboratory X-ray diffractometers.

Accepted 1 May 2020

Dynamical X-ray diffraction imaging of voids in dislocation-free high-purity germanium single crystals

White beam X-ray topography has been performed to provide direct evidence of micro-voids in dislocation-free high-purity germanium single crystals. A general method is proposed to verify the presence of voids for any crystalline material of high structural perfection.

Accepted 30 April 2020

Crystallography of γ′-Fe4N formation in single-crystalline α-Fe whiskers

The crystallography and mechanism of the early stages of the formation of cubic primitive γ′-Fe4N in single-crystal α-Fe whiskers during gaseous nitriding were investigated by electron microscopy and electron backscatter diffraction. The α–γ′ phase transformation could be observed under simplified conditions owing to the lack of geometric constraints for the transformation.

Accepted 20 April 2020

EDDIDAT: a graphical user interface for the analysis of energy-dispersive diffraction data

EDDIDAT is a program that provides a graphical user interface for the evaluation of energy-dispersive X-ray diffraction data with the focus on depth-resolved residual stress analysis.

more ...
Journal logoJournal of Synchrotron Radiation Journal of
Synchrotron Radiation

Accepted 26 May 2020

A helium mini-cryostat for the nanoprobe beamline ID16B at the ESRF: characteristics and performance

This paper reports on the design, implementation, and tests of a He mini-cryostat for the nanoprobe beamline ID16B at the ESRF, and presents the first experimental results obtained using the cryogenic equipment.

Accepted 22 May 2020

Genuine-field modeling of partially coherent X-ray imaging systems

A genuine representation of the cross-spectral density function is applied to model partially coherent wave propagation in X-ray imaging systems.

Accepted 22 May 2020

Generation of an X-ray nanobeam of a free-electron laser using reflective optics with speckle interferometry

Focusing of an X-ray free-electron laser enables the production of ultrahigh-intensity X-ray pulses. X-ray nanobeams of a free-electron laser were generated using reflective focusing optics combined with speckle interferometry.

Accepted 21 May 2020

Large field-of-view scanning small-angle X-ray scattering of mammalian cells

A fast-scanning small-angle X-ray scattering study of biological cells is presented that achieves higher throughput and requires lower dose than previous experiments.

Accepted 20 May 2020

Accurate contrast determination for X-ray speckle visibility spectroscopy

A numerical model that can mimic closely the behavior of real X-ray detectors in the context of X-ray speckle visibility spectroscopy is described. Using this model, this work investigates the origin of discrepancies between commonly used photon locating algorithms and proposes a calibration routine to resolve the discrepancy.

Accepted 20 May 2020

X-ray phase contrast tomography for the investigation of amyotrophic lateral sclerosis

Ex vivo X-ray phase contrast tomography of amyotrophic lateral sclerosis of a SOD1G93A mouse model is presented. Quantification of neuronal and vascular alteration in the central nervous system is described.

Accepted 19 May 2020

Nanoscale element behavior in a continuum


Accepted 19 May 2020

Development of a high-precision XYZ translator and estimation of beam profile of the vacuum ultraviolet and soft X-ray undulator beamline, BL-13B, at the Photon Factory

To enable microscopic measurements at the BL-13B beamline of the Photon Factory, a high-precision XYZ translator is developed, and the beam profile is estimated.

Accepted 19 May 2020

Investigation of third-order nonlinear dynamical X-ray diffraction based on a new exact solution

A new exact solution for the case of third-order nonlinear two-wave X-ray dynamical diffraction is obtained and the third-order nonlinear dynamical diffraction phenomenon is investigated. The solution is presented via Jacobi elliptic functions and takes into account the intensity of the incident wave as well as the deviation from the Bragg exact orientation.

Accepted 15 May 2020

Design of an online spectrometer for the diagnosis of free-electron lasers

An online spectrometer with plane variable-line-spacing grating has been designed to monitor each single free-electron laser pulse, especially for the energy region from 800 to 1000 eV.

more ...
Journal logoIUCrData
IUCrData

Accepted 5 June 2020

1-Benzyl-3-methyl­imidazolium bromide

The mol­ecular structure of the title compound, (BenzMIm)Br (BenzMIm=1-benzyl-3-methyl­imidazolium), consists of separated bromide anions and 1-benzyl-3-methyl­imidazolium cations connected via short C—H⋯Br contacts.

Accepted 4 June 2020

(E)-2-(3,5-Di­meth­oxy­benzyl­idene)indan-1-one

The title compound was prepared via a Claisen-Schmidt condensation through a solventless, green synthesis technique. The resulting crystals formed in the monoclinic space group P21/c, and adopting the common E configuration.


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