forthcoming articles

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

IUCrJ
Accepted 14 October 2020

Complex Imaging of Phase Domains by Deep Neural Network

Abstract Machine Learning approaches can greatly facilitate Single Particle Imaging experiments at XFEL facilities by providing real-time images from the coherent X-ray diffraction data stream, using methods presented in this article.

Accepted 7 October 2020

Molecular-replacement phasing using predicted protein structures from AWSEM-Suite

This paper describes and evaluates the performance of AWSEM-Suite, a force field that includes template-guided refinement and coevolutionary information within the framework of the energy-landscape theory, in using molecular replacement to solve the phase problem by the de novo prediction of structures. It also highlights and discusses how AWSEM-Suite provides better predictions than I-TASSER-MR or the previous algorithm AWSEM-Template.

Accepted 3 October 2020

Cortisone and cortisol break hydrogen-bonding rules to make a drug–prodrug solid solution

In order to form a solid solution with its prodrug cortisone, hydrocortisone (cortisol) must violate Etter's rule of hydrogen bonding. The preparation of a uniform product with the desired composition, which is hindered under a thermodynamic regime, can be achieved by supercritical assisted spray drying. The new phase enables fine-tuning of the phase's composition as well as a higher dissolution rate for hydrocortisone.

Accepted 1 October 2020

Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography

A microcrystal-prelocation method is demonstrated using low-dose 2D full-field propagation-based X-ray phase-contrast imaging on samples with an essentially flat geometry for automated serial crystallography data collection at a microfocus macromolecular crystallography beamline.

Accepted 29 September 2020

Enhancing the signal-to-noise ratio and generating contrast for cryo-EM images with convolutional neural networks

It is demonstrated that a convolutional neural network denoising algorithm can be used to significantly enhance the signal-to-noise ratio and generate contrast in cryo-EM images. It also provides a quantitative evaluation of the bias introduced by the denoising procedure and its influence on image processing and three-dimensional reconstructions.

Accepted 27 September 2020

Photocrystallographic and spectroscopic studies of a model (N,N,O)-donor square-planar nickel(II) nitro complex: in search of high-conversion and stable photoswitchable materials

A new, cheap, easy-to-synthesize and air-stable photoswitchable nickel nitro complex, in which the central metal atom is additionally chelated by a [2-methyl-8-amino­quinoline]-1-tetralone ligand, is reported. The compound was shown to undergo full light-induced isomerization from the nitro to nitrito form by irradiation with a 530–660 nm LED light at 160 K, whereas the generated linkage isomer exhibits thermal stability up to around 230 K.

Accepted 23 September 2020

Beyond integration: modeling every pixel to obtain better structure factors from stills

A pixel-based approach for extracting structure factors from X-ray free-electron laser crystal diffraction measurements is presented.
Journal logoActa Crystallographica Section A
Acta Crystallographica
Section A
FOUNDATIONS AND ADVANCES

Accepted 22 September 2020

Spiral tetrahedral packing in the β-Mn crystal as symmetry realization of the 8D E8 lattice

The 2D projection of all atomic positions in the β-Mn unit cells shows that they are situated on three circumferences containing 2D projections of 90 vertices of the {3, 3, 5} polytope on the same plane. The exhaustive description of the non-crystallographic symmetry of the β-Mn crystal has been achieved by using the 8D E8 lattice in which both the 4D {3, 3, 5} polytope and cubic 6D B6 lattice can be inserted.

Accepted 21 September 2020

Indexing of diffraction patterns for determination of crystal orientations

A general approach to indexing of diffraction patterns originating from crystals of known structures is presented. Example algorithms are shown to be applicable to patterns of various types, e.g., Kikuchi patterns, Kossel patterns or Laue patterns.

Accepted 21 September 2020

Isogonal non-crystallographic periodic graphs based on knotted sodalite cages

Knotted and linked zeolite framework types, based on the sodalite cage (truncated octahedron), are described. Such structures exhibit non-crystallographic symmetry.

Accepted 25 August 2020

Embedding parallelo­hedra into primitive cubic networks and structural automata description

It is proved that any parallelo­hedron P as well as tiling by P, except the rhombic dodeca­hedron, can be embedded into the 3D pcu net. It is proved that for the rhombic dodeca­hedron, embedding into the 3D pcu net does not exist; however, embedding into the 4D pcu net does exist. For each parallelo­hedron the deterministic finite automaton is developed which models the growth of the crystalline structure with the same combinatorial type as the given parallelo­hedron.

Accepted 11 August 2020

Electron image contrast analysis of mosaicity in rutile nanocrystals using direct electron detection

High-resolution electron microscopy image contrast obtained from a rutile nanocrystal using direct electron detection is quantified and interpreted based on a model of mosaic crystals.
Journal logoActa Crystallographica Section B
Acta Crystallographica
Section B
STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS

Accepted 6 October 2020

Cation distribution in Cu2ZnSnSe4, Cu2FeSnS4 and Cu2ZnSiSe4 by multiple-edge anomalous diffraction

Multiple-Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Application of this technique confirms established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS), but in Cu2ZnSiSe4 (CZSiSe) the cation distribution is shown to adopt a highly ordered wurtz-kesterite structure type in contrast to the literature.

Accepted 3 October 2020

Structure and stability of γ1-AuZn2.1: a γ-brass-related complex phase in the Au–Zn System

The synthesis, crystal structure and stability of the γ-brass-related complex phase γ1-AuZn2.1 in the Au–Zn birnary system are reported. The compound has been described as consisting of two main building units, i.e. a 38-atom modified Pierce cluster and an intergrown 19-atom double icosahedron.

Accepted 2 October 2020

Charge density analysis of abiraterone acetate

Experimental charge density distribution of abiraterone acetate is reported. Intermolecular interactions in the crystals of abiraterone, abiraterone acetate and abiraterone complexes with cytochrome P450 binding pocket are compared.

Accepted 16 September 2020

The first bis­muth borate oxyiodide, Bi4BO7I: commensurate or incommensurate?

The first bis­muth borate oxyiodide, Bi4BO7I, is incommensurately modulated with q = 0.242 (3)c*. The wavevector is very close to the rational value of c*/4, yet refinement based on commensurate modulation faces essential[serious] problems indicating the incommensurate nature of the modulation.

Accepted 9 September 2020

A cocrystal of L-ascorbic acid with picolinic acid: the role of O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds and L-ascorbic acid con­formation in structure stabilization

A new cocrystal of L-ascorbic and picolinic acids is reported. The relationship between the con­formation of the L-ascorbic acid molecule and its effective charge in the new cocrystal, as well as in pure ascorbic acid and 12 previously documented L-ascorbic acid cocrystals, is discussed.

Accepted 8 September 2020

Pressure-induced Pb–Pb bonding and phase transition in Pb2SnO4

The structure of Pb2SnO4 is found to strongly distort on compression and a structural phase transition with a change of space group from Pbam to Pnam occurs at ∼11 GPa. Our complementary DFT-based calculations show that at ambient conditions, the channels in the structure host the stereochemically active Pb 6s2 lone electron pairs which form bonds between the Pb atoms with increasing pressure.

Accepted 2 September 2020

A new look at two polymorphic crystal structures of di­benzoyl­methane: relationship between the crystal packing and the hydrogen atom position revealed by quantum chemistry and quantum crystallography methods

Journal logoActa Crystallographica Section C
Acta Crystallographica
Section C
STRUCTURAL CHEMISTRY

Accepted 13 October 2020

Two new CdII MOFs of 1,4-bis­(1H-benzimidazol-1-yl)butane and flexible di­carboxyl­ate ligands: luminescence sensing towards Fe3+

Two new CdII MOFs based on 1,4-bis­(1H-benzimidazol-1-yl)butane and pimelate/sebacate (Pim/Seb) mixed ligands have been synthesized under hydro­thermal conditions. Structure analysis reveals that the Pim MOF is a 2D sql layer structure containing a (H2O)8 water cluster. The Seb MOF shows an 8-connected hex supramolecular structure based on the hxl layer. Luminescence sensing studies reveal that both MOFs have good selectivity and sensitivity for the detection of the Fe3+ cation in water.
Journal logoActa Crystallographica Section D
Acta Crystallographica
Section D
STRUCTURAL BIOLOGY

Accepted 19 October 2020

A Life among Men, Women and Molecules. Memoirs of an Indian Scientist. By MaMannaMana Vijayan. Indian National Science Academy, 2020. Ebook, pp. xi+305. ISBN 978-81-939482-6-2. Price USD 35.00 INR 1500.

A review of the autobiography of one of India's the most important scientists, MaMannaMana Vijayan.

Accepted 15 October 2020

Crystallographic binding studies of rat peroxisomal multifunctional enzyme type-1 (MFE1) with 3-keto­decanoyl-CoA: capturing active and inactive states of its hydratase and de­hydrogenase catalytic sites

The 1.7 Å resolution crystal structure of MFE1 shows a conformation in which both catalytic sites are incompetent. The analysis of the structures of the complexes with 3-ketodecanoyl-CoA suggests how the conformational flexibility of MFE1 could be important for its function.

Accepted 14 October 2020

Low-resolution structures of modular nanotransporters shed light on their functional activity

Abstract Our artificial multifunctional polypeptide construct (modular nanotransporters, MNT) has a great potential in the treatment of various diseases, particularly cancer. In this study 3D low-resolution structure of the MNT in solution was obtained by atomic force microscopy, transmission electron microscopy and small angle X-ray scattering coupled to size exclusion chromatography methods.

Accepted 14 October 2020

Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293S cell line enable diffraction-quality crystallogenesis

Structural studies on glycoproteins are often complicated by glycan complexity. We show that the GlycoDelete HEK cell line enginered to produce glycan stumps produces homogeneous glycoproteins ideal for crystallogenesis and other structural studies.

Accepted 13 October 2020

The copper(II)-binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography

A novel 3 residue tag containing the residues GHK that can be used to promote crystallization and in SAD phasing experiments using its tightly bound copper ion.

Accepted 12 October 2020

Development and Assessment of CootVR, a Virtual Reality Computer Program for Model Building

Virtual reality-specific tools for model building are possible, and can provide order-of-magnitude speedup over mouse-and-keyboard tools in certain situations.

Accepted 8 October 2020

Arginine off-kilter: guanidinium is not as planar as restraints denote

The geometry of arginine shows more complexity than the standard restraints accommodate.

Accepted 7 October 2020

The crystal structure of AjiA1 shows a novel structural motion mechanism in the adenylate-forming enzyme family

AjiA1 is an adenylate-forming enzyme (AFE) family member that catalyzes the condensation of two molecules of 3-hydroxyanthranilic acid using ATP as a co-substrate. The structure of AjiA1 in its apo form was solved and revealed key conformational changes, including an unusual loop swapping, suggesting that it should be classified into a new AFE subgroup.

Accepted 29 September 2020

Real-space quantum-based refinement for cryo-EM: Q|R#3

The implementation of quantum-based real-space refinement in qr.refine is described.

Accepted 29 September 2020

Shift-field refinement of macromolecular atomic models

Shift-field refinement is an approach to the refinement of a model against a set of structure-factor observations which is not tied to an underlying atomic parameterization. The performance of the method is evaluated for the refinement of positional parameters over a set of 452 molecular-replacement problems.

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Journal logoActa Crystallographica Section E
Acta Crystallographica
Section E
CRYSTALLOGRAPHIC COMMUNICATIONS

Accepted 13 October 2020

Synthesis, crystal structure, Hirshfeld surface analysis, MEP study and mol­ecular docking of N-{3-[(4-meth­oxy­phen­yl)carbamo­yl]phen­yl}-3-nitro­benzamide as a promising inhibitor of hfXa

The structure of the title compound is stabilized by the presence of N—H⋯O and C—H⋯O hydrogen bonds. Other inter­actions such as C—H⋯π are also important in the analysis of the Hirshfeld surface. Mol­ecular docking studies show this compound to be a potential anti­coagulant agent.

Accepted 13 October 2020

Crystal structure of the unusual coordination polymer catena-poly[[gold(I)-μ-1,2-bis­(di­phenyl­phosphino­thio­yl)ethane-κ2S:S′] di­bromido­aurate(I)]

In the title compound, the gold(I) centres of the cation are coordinated by the P=S groups of the di­sulfide ligands to form a chain polymer parallel to the c axis. Both independent gold atoms lie on the same twofold axis, and the midpoint of the H2C—CH2 bond lies on an inversion centre. The anions flank the polymeric chain; they are connected to it by short aurophilic inter­actions and C—H⋯Br contacts, and to each other by Br⋯Br contacts.
Journal logoActa Crystallographica Section F
Acta Crystallographica
Section F
STRUCTURAL BIOLOGY COMMUNICATIONS

Accepted 18 October 2020

Chitoporin from Serratia marcescens: recombinant expression, purification and crystallization

Crystallization of chitoporin from Serratia marcescens

Accepted 17 October 2020

The A component (SmhA) of a tripartite pore forming toxin from Serratia marcescens: expression, purification, and crystallographic analysis

Seleno-methionine crystallization of the A-component of the tripartite haemolytic -pore forming toxin from Serratia marcescens.

Accepted 13 October 2020

Crystal structure of GDP-bound GTPase domain of Rab5a from Leishmania donovani

Leishmania donovani Rab5a (LdRab5a), a GTP-dependent molecular switch, regulates the fluid phase endocytosis of essential nutrients. We have determined the crystal structure of the GTPase domain of LdRab5a in the GDP-bound form, which shows the canonical Rab fold but with a unique disposition of the Switch I region.

Accepted 13 October 2020

Structural characterization of a nonhydrolyzing UDP-GlcNAc 2-epimerase from Neisseria meningitidis serogroup A

The crystal structures of the bacterial non-hydrolyzing UDP-GlcNAc 2-epimerase with and without substrates are described. The structures, together when compared to homologous enzymes, shed additional light on the mechanism and understanding of the non-allosteric nature of the enzyme.

Accepted 5 October 2020

Structural and biochemical characterization of the class II fructose-1,6-bis­phosphatase from Francisella tularensis

The structure of the class II fructose-1,6-bisphosphatase from F. tularensis is presented together with kinetic data for the wild type and the active-site mutant Thr89Ser. The structure reveals a tetramer of four identical subunits with approximate 222 symmetry. The structure is related to the homologous structure from the related pathogen Mycobacterium tuberculosis.

Accepted 5 October 2020

X-ray structure analysis of a unique D-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA

The D-amino-acid oxidase from the thermophilic fungus R. emersonii strain YA (ReDAAO) has a high thermal stability and a unique broad substrate specificity. In this study, in order to understand the structural factors that contribute to its unique characteristics, ReDAAO was crystallized and its crystal structure was determined.
Journal logoJournal of Applied Crystallography Journal of Applied
Crystallography

Accepted 13 October 2020

High-Pressure Sapphire Capillary Cell for Synchrotron Single Crystal X-Ray Diffraction Measurements to 1500 bar

Abstract An in-situ single-crystal X-ray diffraction sapphire capillary pressure cell capable of generating 1500 bar of pressure is presented and tested by comparing the compressibility of the small organic molecule hexa­methyl­enetetramine, in its hydrogenated and deuterated forms.

Accepted 11 October 2020

DLSR: A solution to the parallax artefact in X-ray diffraction computed tomography data

A new reconstruction approach is presented that can directly yield physico-chemical images and overcome the parallax problem in X-ray diffraction computed tomography (XRD-CT) experiments.

Accepted 8 October 2020

Instrumentation and Experimental Procedures for Robust Collection of X-ray Diffraction Data from Protein Crystals across Physiological Temperatures

This paper describes a widely applicable protein X-ray crystallography method that enables the collection of high-quality diffraction data from single crystals across a wide range of temperatures at and above room temperature.

Accepted 6 October 2020

ATSAS 3.0: Expanded functionality and new tools for small-angle scattering data analysis

ATSAS is a comprehensive software suite for the processing, visualization, analysis and modelling of small-angle scattering data. This article describes developments in the ATSAS 3.0 release, including new programs for data simulation, and for the structural modelling of lipids, nucleic acids and polydisperse systems.

Accepted 26 September 2020

Application of precise neutron focusing mirrors for neutron reflectometry: latest results and future prospects

A large-area focusing supermirror manufactured with ultra-precision machining has been employed at the SOFIA reflectometer at the J-PARC Materials and Life Science Experimental Facility, and a gain of approximately 100% in the neutron flux was achieved. For future upgrade, optics using the focusing mirror for multi-incident-angle neutron reflectometry are proposed, in order to reveal evolutions of interfacial structures for operando measurements with a wide reciprocal space.

Accepted 25 September 2020

The Cambridge Structural Database in chemical education: analysis of hydrogen bonded networks in salts of hexa-aqua metal ions with organic counterions

This contribution describes a ten-year experience of teaching a computer-based inorganic chemistry laboratory course for undergraduates. The course aims at introducing students to structure analysis of simple inorganic molecular solids with a pragmatic approach. Atomic coordinates of molecular crystals and advanced visualization methods available in the Cambridge Structural Database and its inherent software allow students to link newly apprehended crystallographic skills with knowledge acquired in former basic courses in inorganic, organic, and physical chemistry.

Accepted 21 September 2020

Multiple Epitaxial Lateral Overgrowth of GaN Thin Films Using a Patterned Graphene Mask by Metal Organic Chemical Vapor Deposition

We grew a fully merged multiple-ELOG GaN with only a thickness of several hundred nanometres with self-decomposing graphene during the growth process. Furthermore, the mechanism of multiple-ELOG through self-decomposing graphene due to GaN template decomposition during homoepitaxy was proposed

Accepted 17 September 2020

Unravelling the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ mixed ionic electronic conductors

The crystal structures of non-substituted and Mo-substituted neodymium tungstates are described in detail through neutron diffraction and high-resolution X-ray diffraction. Combined X-ray and neutron diffraction refinements and electron probe micro-analysis were employed to locate Mo atoms in the crystal structure of Nd6−yW1−zMozO12−δ (z = 0, 0.25), while X-ray absorption spectroscopy in the near-edge regions confirmed no changes in the oxidation states of Nd and W.
Journal logoJournal of Synchrotron Radiation Journal of
Synchrotron Radiation

Accepted 30 September 2020

Multi-analyser detector (MAD) for high-resolution and high-energy powder X-ray diffraction

The layout and performance of a multi-analyser detector for high-resolution powder diffraction at an X-ray energy of 60 keV is described.

Accepted 21 September 2020

Fast convolution-based performance estimation method for diffraction-limited source with imperfect X-ray optics

A theoretical approach is proposed to describe the performance degradation caused by imperfect X-ray optical elements.

Accepted 21 September 2020

Nanoparticle dose enhancement of synchrotron radiation in PRESAGE dosimeters

The physical absorbed dose enhancement due to the presence of gold and bis­muth nanoparticles by synchrotron X-ray beams was measured in PRESAGE dosimeters.

Accepted 18 September 2020

Small Bragg-plane slope errors revealed in synthetic diamond crystals

X-ray rocking curve imaging is used to study the smallest achievable Bragg-plane slope errors in the best presently available synthetic diamond crystals and how they compare with those of perfect silicon crystals

Accepted 16 September 2020

Backside-illuminated scientific CMOS detector for soft X-ray resonant scattering and ptychography

This paper reports measurement results and an experimental demonstration of a new backside-illuminated scientific CMOS sensor for soft X-ray experiments at the SOLEIL synchrotron.

Accepted 14 September 2020

Local structure change of luminescent Ag zeolite-A and -X studied by in situ XAFS and IR spectroscopy

Local structure changes of luminescent Ag zeolite-A and -X are analysed by in situ XAFS. The relation between the behaviour of the Ag cluster in the cavity of zeolite and the intensity of the photoluminescence is given.

Accepted 10 September 2020

Zernike phase-contrast full-field transmission X-ray nanotomography for 400 micrometre-sized samples

A method for sub-millimetre field-of-view full-field X-ray tomography at a resolution of hundreds of nanometres is presented.

Accepted 7 September 2020

A coded aperture microscope for X-ray fluorescence full-field imaging

First results from a 10 µm MURA coded aperture optic for a full-field X-ray fluorescence microscope are presented.

Accepted 3 September 2020

Theoretical spectral analysis of FEL radiation from multi-harmonic undulators

A comparative theoretical analysis of the free-electron laser (FEL) radiation in main FEL experiments is given. It is shown that an elliptic undulator with field harmonics and electron–photon phase-shifting yields significantly higher harmonic power than that from a planar undulator with phase-shifting.

Accepted 2 September 2020

Focusing a round coherent beam by spatial filtering the horizontal source


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Journal logoIUCrData
IUCrData

Accepted 19 October 2020

(8-Hy­droxy-6-meth­oxy-1-oxo-1H-isochromen-3-yl)methyl formate: a supra­molecular framework

In the crystal of the title compound, mol­ecules are linked by C—H⋯O hydrogen bonds and a C—H⋯π inter­action, forming a supra­molecular framework.

Accepted 16 October 2020

6-[(2-Hy­droxy-5-methyl­anilino)methyl­idene]-4-nitro­cyclo­hexa-2,4-dien-1-one

The title compound is nearly planar with a dihedral angle between the aromatic rings of 1.41 (8)°. The phenolic O atom is deprotonated and the N atom of the azomethine unit carries the proton, thereby forming an intra­molecular N—H⋯O hydrogen bond. In the crystal, the mol­ecules form inversion dimers via pairwise O—H⋯O hydrogen bonds.

Accepted 15 October 2020

7-Meth­oxy­penta­cyclo­[5.4.0.02,6.03,10.05,9]undec­ane-8,11-dione

The crystal structure of a meth­oxy-substituted Cookson's dione derivative is presented.

Accepted 5 September 2020

Ethyl 3,4-bis­(acet­yloxy)-2-(4-meth­oxy­phen­yl)pyrrol­idine-1-carboxyl­ate

The title compound features a twisted, tetra-substituted pyrrolidine ring, and has an N-bound ethyl­carboxyl­ate substituent with the N atom flanked by a methyl­ene group on one side and a C-bound 4-meth­oxy­phenyl group on the other. These carbon atoms are linked by two methine carbon atoms, each of which bears an acet­yloxy substituent.


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