Book review

The Python-based program py_convrot is a universal converter of rigid-body rotation parameters. The program interactively illustrates the action of various rotation parameters and can be used both for teaching goals and for practical applications.

An X-ray cross-correlation study of the impact of ligand composition and salt content on the self-assembly of soft-shell nanoparticles is presented, indicating symmetry-selective formation of order.

Several oils were examined for use in the cleaning and cryoprotection of crystals in the lipidic cubic phase in terms of their effect on the crystal stability, the background scattering and the facilitation of the experiment.

Because researchers do not understand the formation mechanism of cocrystals, the preparation of cocrystals is mostly done by trial and error. This study focuses on the cocrystal formation mechanism to improve the efficiency of cocrystal preparation.

By using small-angle neutron scattering (SANS) reinforced by scanning electron microscopy, the fine structure of catalysts for polymer electrolyte fuel cells has been investigated. The experimental data resulting from contrast variation with mixed light and heavy water (H2O/D2O) are well described by a core–shell model with fluctuations in concentration between water and Nafion.

The sin2ψ and cosα methods are compared via diffracting-grain identification from electron backscatter diffraction maps. Artificial textures created by the X-ray diffraction measurements are plotted and X-ray elastic constants of the diffracting-grain sets are computed.

Book review

This paper reports on the two-scale fractal structure of chromatin organization in the nucleus of the HeLa cell.

An attempt has been made to combine small-angle scattering of X-rays or neutrons with scanning electron microscopy in reciprocal space, in order to establish a structural analysis method covering a wide range of sizes from micro- to macro-scales.

Book review

A comprehensive analysis focused on Sn segregation during the Ni/GeSn solid-state reaction was carried out. It was demonstrated that Sn is soluble in the various Ni/GeSn intermetallic phases and that, when the temperature increases, the Sn segregation occurs first at grain boundaries, which can hamper Ni diffusion and delay the intermetallic formation.

A fast and exact algorithm to calculate the powder pair distribution function (PDF) for the case of periodic structures is presented. The algorithm especially improves X-ray and electron PDF calculations, and the handling of instrumental resolution functions.

SVAT4 is a computer program for interactive visualization of three-dimensional crystal structures. A wide range of functions are available for structural analysis.

A portable small-angle X-ray scattering instrument with geometrical dimensions suitable for installation at the D22 instrument was designed and constructed for simultaneous small-angle X-ray and neutron scattering experiments at ILL.

An algorithm, based on the matching of q-vectors pairs, is combined with three-dimensional pattern matching using a nearest-neighbors approach to index Laue and monochromatic serial crystallography data recorded on small unit cell samples.

A software package for Grazing Incident Wide Angle X-ray Scattering (GIWAXS) geared toward weakly ordered materials, including: scattering intensity normalization/uncertainty, scattering pattern indexing, and refractive shift correction.

The crystal structure of the organic pigment 2-monomethyl-quinacridone (Pigment Red 192, C21H14N2O2) was solved from X-ray powder diffraction data. The resulting average structure is described in space group Poverline 1, Z = 1 with the molecule on the inversion centre. The molecules are arranged in chains. The molecules, which have no inversion symmetry, show orientational head-to-tail disorder. In the average structure, the methyl group is disordered and found on both ends of the molecule with an occupancy of 0.5 each. The disorder and the local structure were investigated using various ordered structural models. All models were analysed by three approaches: Rietveld refinement, structure refinement to the pair distribution function (PDF) and lattice-energy minimization. All refinements converged well. The Rietveld refinement provided the average structure and gave no indication of a long-range ordering. The refinement to the PDF turned out to be very sensitive to small structural details, giving insight into the local structure. The lattice-energy minimizations revealed a significantly preferred local ordering of neighbouring molecules along the [0ar 11] direction. In conclusion, all methods indicate a statistical orientational disorder with a preferred parallel orientation of molecules in one direction. Additionally, electron diffraction revealed twinning and faint diffuse scattering.

This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z' = 1 polymorph (form II), crystallize in P21/c and P1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z' = 2 polymorph. In addition, cases of serendipitous agreement in terms of 1H or 13C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination.

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (dmin ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) applied through DiSCaMB software library in the structure refinement against X-ray diffraction data largely improves the X—H bond lengths and make them comparable to the averaged neutron bond lengths.

Most articles dealing with R2TSi3 compounds are only interested in one specific composite or in a series of composites with varying T elements while keeping R fixed (or vice versa). The present work gives an overview of the complete range of 2:1:3 silicides, similar those of Hoffmann & Pöttgen (2001) and Pan et al. (2013). In contrast to the work of Hoffmann & Pöttgen (2001), reasons for formation of the different symmetries and superstructures are discussed. Here, crystallographic properties are in[the] focus, whereas physical and magnetic properties are omitted because those are given by Pan et al. (2013). READS LIKE AN ABSTRACT, please re-write and remove references if possible. Should be two sentences max.

The crystal structure of the nanocrystalline pigment mono­methyl-quinacridone was solved from X-ray powder data. The orientational disorder was investigated using Rietveld refinements, structure refinement to the pair-distribution function, and lattice-energy minimizations of various ordered structural models.

The synthesis, characterization and study of structures from a series of bi­phenyls substituted at positions 3, 3', 4 and 4' with groups connected to the bi­phenyl core through oxygen atoms are presented here. The molecular conformation is extensively studied both in the solid as well as in the liquid state, and the effect of different actors (such as packing and chain length) on the torsion angle between aromatic rings is analyzed.

A new ZnII metallocryptand is presented, with an unprecedented diflexure helix.

Crystal structure and microscopic optical properties of anthracene derivative compounds have been investigated by single-crystal synchrotron X-ray diffraction, laser confocal microscopy and fluorescence lifetime imaging microscopy.

Insights were obtained into the structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway for the biosynthesis of lysine.

This article reports conformational polymorphisms of the EF-hand protein MCFD2 which is involved in glycoprotein transport..

The structure of the Pseudomonas aeruginosa T6SS PldB immunity protein PA5086 is reported at 1.9 Å resolution. Comparison of PA5086 with its homologs PA5087 and PA5088 showed great similarities in sequence and structure, but vast divergences in electrostatic potential surfaces.

Aerobic thermoacidophilic archaea belonging to the genus Sulfolobus harbor peroxiredoxins, thiol-dependent peroxidases that assist in protecting the cells from oxidative damage. Here, the crystal structure of the 1-Cys peroxiredoxin from Sulfolobus islandicus, named 1-Cys SiPrx, is presented. A 2.75 Å resolution data set was collected from a crystal belonging to space group P212121, with unit-cell parameters a = 86.8, b = 159.1, c = 189.3 Å, α = β = γ = 90°. The structure was solved by molecular replacement using the homologous Aeropyrum pernix peroxiredoxin (ApPrx) structure as a search model. In the crystal structure, 1-Cys SiPrx assembles into a ring-shaped decamer composed of five homodimers. This quaternary structure corresponds to the oligomeric state of the protein in solution, as observed by size-exclusion chromatography. 1-Cys SiPrx harbors only a single cysteine, which is the peroxidatic cysteine, and lacks both of the cysteines that are highly conserved in the C-terminal arm domain in other archaeal Prx6-subfamily proteins such as ApPrx and that are involved in the association of dimers into higher-molecular-weight decamers and dodecamers. It is thus concluded that the Sulfolobus Prx6-subfamily protein undergoes decamerization independently of arm-domain cysteines.

The structure of a 22-base-pair RNA helix with mismatched pyrimidine base pairs is reported. The helix contains two symmetry-related CUG sequences: a triplet-repeat motif implicated in myotonic dystrophy type 1. The CUG repeat contains a U–U mismatch sandwiched between Watson–Crick pairs. Additionally, the center of the helix contains a dimerized UUCG motif with tandem pyrimidine (U–C/C–U) mismatches flanked by U–G wobble pairs. This region of the structure is significantly different from previously observed structures that share the same sequence and neighboring base pairs. The tandem pyrimidine mismatches are unusual and display sheared, cross-strand stacking geometries that locally constrict the helical width, a type of stacking previously associated with purines in internal loops. Thus, pyrimidine-rich regions of RNA have a high degree of structural diversity.

The membrane protein EsaA is a conserved component of the type VIIb secretion system. Limited proteolysis of purified EsaA from Staphylococcus aureus USA300 identified a stable 48 kDa fragment, which was mapped by fingerprint mass spectrometry to an uncharacterized extracellular segment of EsaA. Analysis by circular dichroism spectroscopy showed that this fragment folds into a single stable domain made of mostly α-helices with a melting point of 34.5°C. Size-exclusion chromatography combined with multi-angle light scattering indicated the formation of a dimer of the purified extracellular domain. Octahedral crystals were grown in 0.2 M ammonium citrate tribasic pH 7.0, 16% PEG 3350 using the hanging-drop vapor-diffusion method. Diffraction data were analyzed to 4.0 Å resolution, showing that the crystals belonged to the enantiomorphic tetragonal space groups P41212 or P43212, with unit-cell parameters a = 197.5, b = 197.5, c = 368.3 Å, α = β = γ = 90°.

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli.

Cytisine, a natural product with high affinity for clinically relevant nicotinic acetylcholine receptors (nAChRs), is used as a smoking-cessation agent. The compound displays an excellent clinical profile and hence there is an interest in derivatives that may be further improved or find use in the treatment of other conditions. Here, the binding of a cytisine derivative modified by the addition of a 3-(hydroxypropyl) moiety (ligand 4) to Aplysia californica acetylcholine-binding protein (AcAChBP), a surrogate for nAChR orthosteric binding sites, was investigated. Isothermal titration calorimetry revealed that the favorable binding of cytisine and its derivative to AcAChBP is driven by the enthalpic contribution, which dominates an unfavorable entropic component. Although ligand 4 had a less unfavorable entropic contribution compared with cytisine, the affinity for AcAChBP was significantly diminished owing to the magnitude of the reduction in the enthalpic component. The high-resolution crystal structure of the AcAChBP–4 complex indicated close similarities in the protein–ligand interactions involving the parts of 4 common to cytisine. The point of difference, the 3-(hydroxypropyl) substituent, appears to influence the conformation of the Met133 side chain and helps to form an ordered solvent structure at the edge of the orthosteric binding site.

Immunoglobulin E (IgE) plays a central role in the allergic response, in which cross-linking of allergen by Fc∊RI-bound IgE triggers mast cell and basophil degranulation and the release of inflammatory mediators. The high-affinity interaction between IgE and Fc∊RI is a long-standing target for therapeutic intervention in allergic disease. Omalizumab is a clinically approved anti-IgE monoclonal antibody that binds to free IgE, also with high affinity, preventing its interaction with Fc∊RI. All attempts to crystallize the pre-formed complex between the omalizumab Fab and the Fc region of IgE (IgE-Fc), to understand the structural basis for its mechanism of action, surprisingly failed. Instead, the Fab alone selectively crystallized in different crystal forms, but their structures revealed intermolecular Fab/Fab interactions that were clearly strong enough to disrupt the Fab/IgE-Fc complexes. Some of these interactions were common to other Fab crystal structures. Mutations were therefore designed to disrupt two recurring packing interactions observed in the omalizumab Fab crystal structures without interfering with the ability of the omalizumab Fab to recognize IgE-Fc; this led to the successful crystallization and subsequent structure determination of the Fab/IgE-Fc complex. The mutagenesis strategy adopted to achieve this result is applicable to other intractable Fab/antigen complexes or systems in which Fabs are used as crystallization chaperones.

The true identity of the protein found in the crystals reported by Bondoc et al. [(2019), Acta Cryst. F75, 646–651] is given.

Each year thousands of vacationers enjoy the scenery along Virginia’s Skyline Drive, little knowing that for a few brief moments they are passing through the territory of an endangered […]

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A recent study of dog bones excavated from archaeological sites on the Channel Islands of California has cast new light on the past ecology of the islands and the impact that domestic dogs--brought to the islands by Native Americans more than 6,000 years ago—may have once had on the islands’ animals and ecosystems.

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It was an exciting and busy 24 hours at the National Zoo’s Conservation and Research Center in Front Royal, Va., last week as three births took place just hours apart. On the evening of July 9, a clouded leopard cub was born, followed by a Przewalski’s horse foal and a red panda cub.

The post Baby Boom of Endangered Species at Smithsonian’s National Zoo’s Conservation and Research Center appeared first on Smithsonian Insider.

The Smithsonian’s National Air and Space Museum has opened a new Public Observatory that contains a 16-inch, 3,000-pound Boller and Chivens telescope, on loan from the Smithsonian Astrophysical Observatory. Through this powerful telescope, museum visitors can now observe the sun (with a special filter), the moon and the brighter stars and planets, such as Venus, Jupiter and Saturn, during daylight hours. Funding for the project was provided by the National Science Foundation.

The post The Smithsonian’s National Air and Space Museum opens new Public Observatory on the Mall in Washington, D.C. appeared first on Smithsonian Insider.

The John Marshall Ju/'hoan Bushman Film and Video Collection, 1950-2000, was among 35 documentary heritage items of exceptional value added to UNESCO’s Memory of the World Register in 2009.

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“Spinning under the influence” is one way to describe recent activities in the Costa Rican laboratory of Smithsonian scientist William Eberhard. An entomologist at the Smithsonian’s Tropical Research Institute, Eberhard recently carried out a series of experiments in which he observed the web-building behavior of dozens of spiders under the influence of drugs—specifically, a chemical injected into their bodies by parasitic wasps.

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Timing was critical because female giant pandas ovulate only once a year. A short period of two to three days around ovulation is the only time she is able to conceive. Gestation typically lasts from 90 to 185 days.

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Birds do it. Bees do it. And in a laboratory in northern California, scientists using bumblebees recently figured out the best way to measure it--vertical lift!

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White, who was a student at Columbian College from Accomack County, Va., died of pneumonia and complications from a mitral heart defect. When his coffin was unearthed, his identity was a deep mystery.

The post Remains of William Taylor White (1837-1852) donated to Smithsonian with his coffin and clothing appeared first on Smithsonian Insider.