This article describes new developments in the CrystalCMP software. In particular, an automatic procedure for comparison of molecular packing is presented. The key components are an automated procedure for fragment selection and the replacement of the angle calculation by root-mean-square deviation of atomic positions. The procedure was tested on a large data set taken from the Cambridge Structural Database (CSD) and the results of all the comparisons were saved as an HTML page, which is freely available on the web. The analysis of the results allowed estimation of the threshold for identification of identical packing and allowed duplicates and entries with potentially incorrect space groups to be found in the CSD.

Total scattering measurements enable understanding of the structural disorder in crystalline materials by Fourier transformation of the total structure factor, S(Q), where Q is the magnitude of the scattering vector. In this work, the direct calculation of total scattering from a crystalline structural model is proposed. To calculate the total scattering intensity, a suitable Q-broadening function for the diffraction profile is needed because the intensity and the width depend on the optical parameters of the diffraction apparatus, such as the X-ray energy resolution and divergence, and the intrinsic parameters. X-ray total scattering measurements for CeO2 powder were performed at beamline BL04B2 of the SPring-8 synchrotron radiation facility in Japan for comparison with the calculated S(Q) under various optical conditions. The evaluated Q-broadening function was comparable to the full width at half-maximum of the Bragg peaks in the experimental total scattering pattern. The proposed calculation method correctly accounts for parameters with Q dependence such as the atomic form factor and resolution function, enables estimation of the total scattering factor, and facilitates determination of the reduced pair distribution function for both crystalline and amorphous materials.

Microcrystal electron diffraction (MicroED) combines crystallography and electron cryo-microscopy (cryo-EM) into a method that is applicable to high-resolution structure determination. In MicroED, nanosized crystals, which are often intractable using other techniques, are probed by high-energy electrons in a transmission electron microscope. Diffraction data are recorded by a camera in movie mode: the nanocrystal is continuously rotated in the beam, thus creating a sequence of frames that constitute a movie with respect to the rotation angle. Until now, diffraction-optimized cameras have mostly been used for MicroED. Here, the use of a direct electron detector that was designed for imaging is reported. It is demonstrated that data can be collected more rapidly using the Falcon III for MicroED and with markedly lower exposure than has previously been reported. The Falcon III was operated at 40 frames per second and complete data sets reaching atomic resolution were recorded in minutes. The resulting density maps to 2.1 Å resolution of the serine protease proteinase K showed no visible signs of radiation damage. It is thus demonstrated that dedicated diffraction-optimized detectors are not required for MicroED, as shown by the fact that the very same cameras that are used for imaging applications in electron microscopy, such as single-particle cryo-EM, can also be used effectively for diffraction measurements.

Protein-engineering methods have been exploited to produce a surrogate system for the extracellular neurotransmitter-binding site of a heteromeric human ligand-gated ion channel, the glycine receptor. This approach circumvents two major issues: the inherent experimental difficulties in working with a membrane-bound ion channel and the complication that a heteromeric assembly is necessary to create a key, physiologically relevant binding site. Residues that form the orthosteric site in a highly stable ortholog, acetylcholine-binding protein, were selected for substitution. Recombinant proteins were prepared and characterized in stepwise fashion exploiting a range of biophysical techniques, including X-ray crystallography, married to the use of selected chemical probes. The decision making and development of the surrogate, which is termed a glycine-binding protein, are described, and comparisons are provided with wild-type and homomeric systems that establish features of molecular recognition in the binding site and the confidence that the system is suited for use in early-stage drug discovery targeting a heteromeric α/β glycine receptor.

Solute carriers are a large class of transporters that play key roles in normal and disease physiology. Among the solute carriers, heteromeric amino-acid transporters (HATs) are unique in their quaternary structure. LAT1–CD98hc, a HAT, transports essential amino acids and drugs across the blood–brain barrier and into cancer cells. It is therefore an important target both biologically and therapeutically. During the course of this work, cryo-EM structures of LAT1–CD98hc in the inward-facing conformation and in either the substrate-bound or apo states were reported to 3.3–3.5 Å resolution [Yan et al. (2019), Nature (London), 568, 127–130]. Here, these structures are analyzed together with our lower resolution cryo-EM structure, and multibody 3D auto-refinement against single-particle cryo-EM data was used to characterize the dynamics of the interaction of CD98hc and LAT1. It is shown that the CD98hc ectodomain and the LAT1 extracellular surface share no substantial interface. This allows the CD98hc ectodomain to have a high degree of movement within the extracellular space. The functional implications of these aspects are discussed together with the structure determination.

Olfactomedins are a family of modular proteins found in multicellular organisms that all contain five-bladed β-propeller olfactomedin (OLF) domains. In support of differential functions for the OLF propeller, the available crystal structures reveal that only some OLF domains harbor an internal calcium-binding site with ligands derived from a triad of residues. For the myocilin OLF domain (myoc-OLF), ablation of the ion-binding site (triad Asp, Asn, Asp) by altering the coordinating residues affects the stability and overall structure, in one case leading to misfolding and glaucoma. Bioinformatics analysis reveals a variety of triads with possible ion-binding characteristics lurking in OLF domains in invertebrate chordates such as Arthropoda (Asp–Glu–Ser), Nematoda (Asp–Asp–His) and Echinodermata (Asp–Glu–Lys). To test ion binding and to extend the observed connection between ion binding and distal structural rearrangements, consensus triads from these phyla were installed in the myoc-OLF. All three protein variants exhibit wild-type-like or better stability, but their calcium-binding properties differ, concomitant with new structural deviations from wild-type myoc-OLF. Taken together, the results indicate that calcium binding is not intrinsically destabilizing to myoc-OLF or required to observe a well ordered side helix, and that ion binding is a differential feature that may underlie the largely elusive biological function of OLF propellers.

Corrections are published for the article by Caldararu et al. [(2019), Acta Cryst. D75, 368–380].

The ePix10ka2M (ePix10k) is a new large area detector specifically developed for X-ray free-electron laser (XFEL) applications. The hybrid pixel detector was developed at SLAC to provide a hard X-ray area detector with a high dynamic range, running at the 120 Hz repetition rate of the Linac Coherent Light Source (LCLS). The ePix10k consists of 16 modules, each with 352 × 384 pixels of 100 µm × 100 µm distributed on four ASICs, resulting in a 2.16 megapixel detector, with a 16.5 cm × 16.5 cm active area and ∼80% coverage. The high dynamic range is achieved with three distinct gain settings (low, medium, high) as well as two auto-ranging modes (high-to-low and medium-to-low). Here the three fixed gain modes are evaluated. The resulting dynamic range (from single photon counting to 10000 photons pixel−1 pulse−1 at 8 keV) makes it suitable for a large number of different XFEL experiments. The ePix10k replaces the large CSPAD in operation since 2011. The dimensions of the two detectors are similar, making the upgrade from CSPAD to ePix10k straightforward for most setups, with the ePix10k improving on experimental performance. The SLAC-developed ePix cameras all utilize a similar platform, are tailored to target different experimental conditions and are designed to provide an upgrade path for future high-repetition-rate XFELs. Here the first measurements on this new ePix10k detector are presented and the performance under typical XFEL conditions evaluated during an LCLS X-ray diffuse scattering experiment measuring the 9.5 keV X-ray photons scattered from a thin liquid jet.

GIDVis is a software package based on MATLAB specialized for, but not limited to, the visualization and analysis of grazing-incidence thin-film X-ray diffraction data obtained during sample rotation around the surface normal. GIDVis allows the user to perform detector calibration, data stitching, intensity corrections, standard data evaluation (e.g. cuts and integrations along specific reciprocal-space directions), crystal phase analysis etc. To take full advantage of the measured data in the case of sample rotation, pole figures can easily be calculated from the experimental data for any value of the scattering angle covered. As an example, GIDVis is applied to phase analysis and the evaluation of the epitaxial alignment of pentacene­quinone crystallites on a single-crystalline Au(111) surface.

A calculation procedure for X-ray total scattering and the pair distribution function from a crystalline structural model is presented. It allows one to easily and precisely deal with diffraction-angle-dependent parameters such as the atomic form factor and the resolution of the optics.

New developments in the program CrystalCMP are presented, and the program is tested on a large number of crystal structures extracted from the Cambridge Structural Database.

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.

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.

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.

A Smithsonian Institution biologist, working with the Natural History Unit of the British Broadcasting Corp., has discovered a new species of giant rat on a film-making expedition to a remote rainforest in New Guinea.

The post New species of giant rat discovered in crater of volcano in Papua New Guinea appeared first on Smithsonian Insider.

Now that astronomers are finding rocky worlds orbiting distant stars, they're asking the next logical questions: Do any of those worlds have volcanoes? And if so, could we detect them? Work by theorists at the Harvard-Smithsonian Center for Astrophysics suggests that the answer to the latter is a qualified "Yes."

The post Can we spot volcanoes on alien worlds? Astronomers say yes appeared first on Smithsonian Insider.

The most widely used methods for calculating species extinction rates are "fundamentally flawed" and overestimate extinction rates by as much as 160 percent, life scientists report May 19 in the journal Nature.

The post Methods for calculating species extinction rates overestimate extinction, says Smithsonian scientist appeared first on Smithsonian Insider.

Collecting trips for Charles Doolittle Walcott (1850-1927), paleontologist and fourth Secretary of the Smithsonian Institution, were often a family affair. This 1910 photograph shows their […]

The post Charles Doolittle Walcott (1850-1927) family campsite in the Canadian Rockies appeared first on Smithsonian Insider.

Halocoryza acapulcana Whitehead (Acapulco Saline Catarrh Beetle), described in 1966 by Donald R. Whitehead. This image is from a recent paper by Terry L. Erwin, […]

The post Halocoryza acapulcana Whitehead appeared first on Smithsonian Insider.

Their research revealed that the types of waterbirds that inhabit urban estuaries are influenced not only by urban development, but also by a far more natural process―rain.

The post Scientists find that rain may not always be a welcome thing to waterbirds appeared first on Smithsonian Insider.

On April 15 the National Museum of Natural History took delivery of a nearly complete Tyrannosaurus rex skeleton. Called the Nation’s T. rex, it will be the centerpiece of […]

The post Smithsonian Welcomes “Nation’s T. rex” to Washington, D.C. appeared first on Smithsonian Insider.

Richard Wunderman is managing editor of the Bulletin of the Global Volcanism Network and a geologist in the Division of Mineral Sciences at the Smithsonian’s […]

The post Q&A: Smithsonian volcanologist Richard Wunderman answers questions about the Aug. 23, East Coast earthquake appeared first on Smithsonian Insider.

Restless volcano. This Feb. 10 satellite radar image shows the summit of Alaska’s Cleveland Volcano and a new lava dome within the volcano’s summit crater […]

The post A restless volcano appeared first on Smithsonian Insider.

According to the weekly report of the Smithsonian’s Global Volcanism Program, gas-and-ash plumes rose nearly one mile above the crater of Mexico’s Popocatépetl volcano from […]

The post Mexico’s Popocatepetl volcano active again appeared first on Smithsonian Insider.

Volcanoes are a source of fascination for many, attracting a steady stream of visitors worldwide. While the danger of sudden eruptions may add to the […]

The post When will a volcano explode, ooze or lie silent? appeared first on Smithsonian Insider.

To get a better idea of just what is going on with the current volcanic eruption of Kilauea on the island of Hawaii, take a […]

The post Kilauea’s activity is nothing new, says a Smithsonian volcano expert appeared first on Smithsonian Insider.

Rick Wunderman of the Global Volcanism Program at the Smithsonian's National Museum of Natural History talks about the current volcanic activity in Iceland.

The post Smithsonian volcanologist Rick Wunderman talks about volcanos and the recent eruptions in Iceland appeared first on Smithsonian Insider.

Smithsonian Scientist Helen James dives into dormant Hawaiian volcanoes to find bird fossils. Her work to identify these species (some new species, some extinct) helps us learn about the past--specifically, how humans might have caused the extinction of certain bird species.

The post Meet Our Scientist–Helen James dives into dormant Hawaiian volcanoes to find bird fossils appeared first on Smithsonian Insider.

The post Learn about the ash that comes from volcanoes with Dr. Liz Cottrell, a geologist from the National Museum of Natural History appeared first on Smithsonian Insider.

myVolcano is a crowd-sourcing app that enables you to share your photographs and descriptions of volcanic hazards, as well as collecting samples and measurements of […]

The post New: myVolcano crowd-sourcing app appeared first on Smithsonian Insider.

Join Dr. Elizabeth Cottrell as she explores the volcanoes of Alaska’s Western Aleutian Islands.

The post Smithsonian volcanologist Elizabeth Cottrell explores Alaskan Volcanoes appeared first on Smithsonian Insider.

Fulcaldea stuessyi is a newly discovered member of the Barnadesioideae, a subfamily of the Compositae, or sunflower family of flowering plants. It was found in northeastern […]

The post Fulcaldea stuessyi is newly discovered member of the Barnadesioideae, a subfamily of the Compositae, or sunflower family of flowering plants, appeared first on Smithsonian Insider.

Diffuse scattering is a rich source of information about disorder in crystalline materials, which can be modelled using atomistic techniques such as Monte Carlo and molecular dynamics simulations. Modern X-ray and neutron scattering instruments can rapidly measure large volumes of diffuse-scattering data. Unfortunately, current algorithms for atomistic diffuse-scattering calculations are too slow to model large data sets completely, because the fast Fourier transform (FFT) algorithm has long been considered unsuitable for such calculations [Butler & Welberry (1992). J. Appl. Cryst. 25, 391–399]. Here, a new approach is presented for ultrafast calculation of atomistic diffuse-scattering patterns. It is shown that the FFT can actually be used to perform such calculations rapidly, and that a fast method based on sampling theory can be used to reduce high-frequency noise in the calculations. These algorithms are benchmarked using realistic examples of compositional, magnetic and displacive disorder. They accelerate the calculations by a factor of at least 102, making refinement of atomistic models to large diffuse-scattering volumes practical.

Crystals of the rare earth metal polytelluride LaTe1.82(1), namely, lanthanum telluride (1/1.8), have been grown by molten alkali halide flux reactions and vapour-assisted crystallization with iodine. The two-dimensionally incommensurately modulated crystal structure has been investigated by X-ray diffraction experiments. In contrast to the tetra­gonal average structure with unit-cell dimensions of a = 4.4996 (5) and c = 9.179 (1) Å at 296 (1) K, which was solved and refined in the space group P4/nmm (No. 129), the satellite reflections are not compatible with a tetra­gonal symmetry but enforce a symmetry reduction. Possible space groups have been derived by group–subgroup relationships and by consideration of previous reports on similar rare earth metal polychalcogenide structures. Two structural models in the ortho­rhom­bic superspace group, i.e. Pmmn(α,β,1 over 2)000(−α,β,1 over 2)000 (No. 59.2.51.39) and Pm21n(α,β,1 over 2)000(−α,β,1 over 2)000 (No. 31.2.51.35), with modulation wave vectors q1 = αa* + βb* + 1 over 2c* and q2 = −αa* + βb* + 1 over 2c* [α = 0.272 (1) and β = 0.314 (1)], have been established and evaluated against each other. The modulation describes the distribution of defects in the planar [Te] layer, coupled to a displacive modulation due to the formation of different Te anions. The bonding situation in the planar [Te] layer and the different Te anion species have been investigated by density functional theory (DFT) methods and an electron localizability indicator (ELI-D)-based bonding analysis on three different approximants. The temperature-dependent electrical resistance revealed a semiconducting behaviour with an estimated band gap of 0.17 eV.

The inversion of X-ray reflectivity to reveal the topography of a one-dimensional interface is evaluated through model calculations.

Most Americans and Canadians up to age 70 need no more than 600 international units (IUs) of vitamin D per day to maintain health, and those 71 and older may need as much as 800 IUs, says a new report from the Institute of Medicine.

Despite broad understanding of volcanoes, our ability to predict the timing, duration, type, size, and consequences of volcanic eruptions is limited, says a new report by the National Academies of Sciences, Engineering, and Medicine.

Despite progress in recent decades, more than 10,000 alcohol-impaired driving fatalities occur each year in the U.S. To address this persistent problem, stakeholders -- from transportation systems to alcohol retailers to law enforcement -- should work together to implement policies and systems to eliminate these preventable deaths, says a new report from the National Academies of Sciences, Engineering, and Medicine.

Individuals can assess how their behaviour is affecting nitrogen pollution with a newly developed nitrogen footprint calculator, which was developed by a team from the University of Virginia (U.S.) and the Energy Research Centre (ECN, the Netherlands). For many people in wealthy countries, reducing protein consumption to the recommended levels and reducing the amount of red meat and energy they consume would significantly lower their nitrogen footprint.

A research group under the leadership of Linköping University Professor Markus Heilig has identified an enzyme whose production is turned off in nerve cells of the frontal lobe when alcohol dependence develops. The deficiency in this enzyme leads to continued use of alcohol despite adverse consequences.

read more

The thinning of Iceland’s ice caps could be influencing volcanic activity, according to new research. The study developed a model to predict the changes in pressure on magma caused by thinning ice and applied it to the recent activity of two Icelandic volcanoes. The results suggest that the effects of thinning ice may increase volcanic activity in some cases, but reduce it in others.

A new study has combined measurements of carbon dioxide (CO2) fluxes with estimates of other greenhouse gas (GHG) emissions from farming operations for 15 European crop sites over several years. It estimated that the sites lost on average 138g of carbon per m2 per year. The total GHG balance (including non-CO2 emissions) was equivalent to an average carbon loss of 203g of carbon per m2 per year.

Researchers have used a new comprehensive life cycle approach to estimate greenhouse gas (GHG) emissions from road construction. When applied to four projects in Spain, the results suggest improvements could be made in the use and efficiency of off-road machinery, the choice of materials and restoration of ecosystems.

A recent overview and analysis shows that increasing amounts of gas drilling at Groningen, the largest gas field in Europe, led to a dramatic rise in regional earthquakes between 2001 and 2013. After a reduction in extraction was introduced by the Dutch Government, earthquake numbers started to fall. Statistical analysis reveals that if high extraction rates were resumed, about 35 earthquakes, with a magnitude (M) of over 1.5 on the Richter scale, might occur annually from the year 2021 onwards, including four with a damaging magnitude of over 2.5.

Storing atmospheric carbon dioxide (CO2) has the potential to mitigate the impacts of changes in climate. Researchers have now developed a way to inject CO2 into volcanic rock, and tested it in Iceland. Over 95% of the injected CO2 was mineralised (converted into a solid) within two years, instead of taking centuries or millennia as previously anticipated. The technique demonstrates potential for the permanent and safe storage of CO2 within basaltic rocks.

Ahuna Mons is a volcano that rises 13,000 feet high and spreads 11 miles wide at its base. This would be impressive for a volcano on Earth. But Ahuna Mons stands on Ceres, a dwarf planet less than 600 miles wide that orbits the Sun between Mars and Jupiter. Even stranger, Ahuna Mons isn't built from lava the way terrestrial volcanoes are -- it's built from ice.

read more