The neutron powder diffractometer POWGEN at the Spallation Neutron Source has recently (2017–2018) undergone an upgrade which resulted in an increased detector complement along with a full overhaul of the structural design of the instrument. The current instrument has a solid angular coverage of 1.2 steradians and maintains the original third-generation concept, providing a single-histogram data set over a wide d-spacing range and high resolution to access large unit cells, detailed structural refinements and in situ/operando measurements.

DatView is a new graphical user interface (GUI) for plotting parameters to explore correlations, identify outliers and export subsets of data. It was designed to simplify and expedite analysis of very large unmerged serial femtosecond crystallography (SFX) data sets composed of indexing results from hundreds of thousands of microcrystal diffraction patterns. However, DatView works with any tabulated data, offering its functionality to many applications outside serial crystallography. In DatView's user-friendly GUI, selections are drawn onto plots and synchronized across all other plots, so correlations between multiple parameters in large multi-parameter data sets can be rapidly identified. It also includes an item viewer for displaying images in the current selection alongside the associated metadata. For serial crystallography data processed by indexamajig from CrystFEL [White, Kirian, Martin, Aquila, Nass, Barty & Chapman (2012). J. Appl. Cryst. 45, 335–341], DatView generates a table of parameters and metadata from stream files and, optionally, the associated HDF5 files. By combining the functionality of several commonly needed tools for SFX in a single GUI that operates on tabulated data, the time needed to load and calculate statistics from large data sets is reduced. This paper describes how DatView facilitates (i) efficient feedback during data collection by examining trends in time, sample position or any parameter, (ii) determination of optimal indexing and integration parameters via the comparison mode, (iii) identification of systematic errors in unmerged SFX data sets, and (iv) sorting and highly flexible data filtering (plot selections, Boolean filters and more), including direct export of subset CrystFEL stream files for further processing.

Errors in the article by Opara, Martiel, Arnold, Braun, Stahlberg, Makita, David & Padeste [J. Appl. Cryst. (2017), 50, 909–918] are corrected.

Grazing-incidence small-angle X-ray scattering (GISAXS) coupled with computed tomography (CT) has enabled the visualization of the spatial distribution of nanostructures in thin films. 2D GISAXS images are obtained by scanning along the direction perpendicular to the X-ray beam at each rotation angle. Because the intensities at the q positions contain nanostructural information, the reconstructed CT images individually represent the spatial distributions of this information (e.g. size, shape, surface, characteristic length). These images are reconstructed from the intensities acquired at angular intervals over 180°, but the total measurement time is prolonged. This increase in the radiation dosage can cause damage to the sample. One way to reduce the overall measurement time is to perform a scanning GISAXS measurement along the direction perpendicular to the X-ray beam with a limited interval angle. Using filtered back-projection (FBP), CT images are reconstructed from sinograms with limited interval angles from 3 to 48° (FBP-CT images). However, these images are blurred and have a low image quality. In this study, to optimize the CT image quality, total variation (TV) regularization is introduced to minimize sinogram image noise and artifacts. It is proposed that the TV method can be applied to downsampling of sinograms in order to improve the CT images in comparison with the FBP-CT images.

An error in the article by Gao, Zhang, Zhu, Wu, Mo, Pan, Liu & Jiang [J. Appl. Cryst. (2019), 52, 637–642] is corrected.

Digitonin has long been used as a mild detergent for extracting proteins from membranes for structure and function studies. As supplied commercially, digitonin is inhomogeneous and requires lengthy pre-treatment for reliable downstream use. Glyco-diosgenin (GDN) is a recently introduced synthetic surfactant with features that mimic digitonin. It is available in homogeneously pure form. GDN is proving to be a useful detergent, particularly in the area of single-particle cryo-electron microscopic studies of membrane integral proteins. With a view to using it as a detergent for crystallization trials by the in meso or lipid cubic phase method, it was important to establish the carrying capacity of the cubic mesophase for GDN. This was quantified in the current study using small-angle X-ray scattering for mesophase identification and phase microstructure characterization as a function of temperature and GDN concentration. The data show that the lipid cubic phase formed by hydrated monoolein tolerates GDN to concentrations orders of magnitude in excess of those used for membrane protein studies. Thus, having GDN in a typical membrane protein preparation should not deter use of the in meso method for crystallogenesis.

This paper reports an Fe-added Y2O3 crucible which is capable of balancing the solution spontaneously and is employed to effectively enhance the homogeneity of YBa2(Cu1−xFex)3O7−δ single crystals.

BEATRIX, is a new tool for performing data analysis of energy-resolved neutron-imaging experiments involving intense fitting procedures of multi-channel spectra. The use of BEATRIX is illustrated for a test specimen, providing spatially resolved 2D maps for residual strains and Bragg edge heights.

The unique nucleating and phasing capabilities of the crystallophore, Tb-Xo4, are illustrated through challenging cases.

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

Book review

The design and assembly of two 3D-printed holders for high-throughput in meso in situ fixed-target crystallographic data collection are described.

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.

Neutron crystal structure analysis of hen egg-white lysozyme hydrogen/deuterium exchanged before crystallization were performed by the joint X-ray and neutron refinement. The differences in hydrogen/deuterium exchange behavior between this study and previous ones were observed.

A detailed study on chiral compound structures found in the Cambridge Structural Database (CSD) is presented. Solvates, salts and co-crystals have intentionally been excluded, in order to focus on the most basic structures of single enantiomers, scalemates and racemates. Similarity between the latter and structures of achiral monomolecular compounds has been established and utilized to arrive at important conclusions about crystallization of chiral compounds. For example, the fundamental phenomenon of conglomerate formation and, in particular, their frequency of occurrence is addressed. In addition, rarely occurring kryptoracemates and scalemic compounds (anomalous racemates) are discussed. Finally, an extended search of enantiomer solid solutions in the CSD is performed to show that there are up to 1800 instances most probably hiding among the deposited crystal structures, while only a couple of dozen have been previously known and studied.

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.

A study on chiral monomolecular compound structures found in the Cambridge Structural Database is presented.

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.

The crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum is reported. It has high structural similarity to other gluconate 5-dehydrogenase proteins, demonstrating that this enzyme is highly conserved.

A putative open reading frame encoding GTP cyclohydrolase I from Listeria monocytogenes was expressed in a recombinant Escherichia coli strain. The recombinant protein was purified and was confirmed to convert GTP to dihydroneopterin triphosphate (Km = 53 µM; vmax = 180 nmol mg−1 min−1). The protein was crystallized from 1.3 M sodium citrate pH 7.3 and the crystal structure was solved at a resolution of 2.4 Å (Rfree = 0.226) by molecular replacement using human GTP cyclohydrolase I as a template. The protein is a D5-symmetric decamer with ten topologically equivalent active sites. Screening a small library of about 9000 compounds afforded several inhibitors with IC50 values in the low-micromolar range. Several inhibitors had significant selectivity with regard to human GTP cyclohydrolase I. Hence, GTP cyclohydrolase I may be a potential target for novel drugs directed at microbial infections, including listeriosis, a rare disease with high mortality.

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.

Describing his project of counting bears, bobcats and other predatory mammals along the Appalachian Trail, National Zoological Park wildlife ecologist William McShea looks to American literature for a comparison.

The post Appalachian Trail survey aims hidden cameras at large predators appeared first on Smithsonian Insider.

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 […]

The post Study aims to give endangered Shenandoah salamander better odds at survival appeared first on Smithsonian Insider.

New measurements show that the Milky Way is bigger and more massive than previous data suggested, putting us on equal footing with our neighbor. Specifically, the Milky Way is 15 percent larger in size and contains 50 percent more mass. That is the cosmic equivalent of a 5-foot-5, 140-pound man suddenly bulking up to the size of a 6-foot-3, 210-pound NFL linebacker.

The post New research reveals our galaxy is much larger than we thought appeared first on Smithsonian Insider.

Scientists at the Smithsonian Institution examined the feather remains from the Jan. 15, 2009, US Airways Flight 1549 bird strike to determine not only the species, but also that the Canada geese involved were from a migratory, rather than resident, population. This knowledge is essential for wildlife professionals to develop policies and techniques that will reduce the risk of future collisions. The team’s findings were published in the journal “Frontiers in Ecology and the Environment” in June.

The post Scientists Determine Geese Involved in Hudson River Plane Crash Were Migratory appeared first on Smithsonian Insider.

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.

Successes in animal health care presents many new challenges for veterinarians. Longer life spans in captivity mean zoo animals are now experiencing age-related health problems that their zoo predecessors never lived long enough to develop—like diabetes in cheetahs, arthritis in big cats and dental issues for coatis.

The post Golden years at the Zoo: Veterinarians work to help animals live longer, stay healthy appeared first on Smithsonian Insider.

A recent survey of the bottom-dwelling animals of the Chesapeake has revealed that communities of even these relatively hardy organisms are under stress. Many regions of the bay are becoming inhospitable to bottom-dwelling animals because of a lack of oxygen—a condition known as “hypoxia.”

The post Bottom-dwelling creatures in the Chesapeake Bay need more oxygen, study finds. appeared first on Smithsonian Insider.

The Smithsonian Center for Education and Museum Studies is hosting “Climate Change,” a three-day, free, education online conference Tuesday, Sept. 29 through Thursday, Oct. 1. This […]

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It is one of the largest and most productive estuaries in the world, yet dramatic changes are in store for the Chesapeake Bay in coming […]

The post Climate change may drastically alter Chesapeake Bay, scientists say appeared first on Smithsonian Insider.

“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.

The post Drugged spiders’ web spinning may hold keys to understanding animal behavior appeared first on Smithsonian Insider.

Koenig and his colleagues examined an area of space called W5, which lies about 6,500 light-years away toward the constellation Cassiopeia—about 6 trillion miles. Their research indicates the prospects for hypothetical alien life there are disappointing.

The post Planets form around many star types, but intelligent life is probably rare appeared first on Smithsonian Insider.

It’s not an exaggeration to say Hedrick was ecstatic when she peered into her inverted phase contrast microscope and found "Amphisolenia quadrispina" floating in her sample. “For 20 years I’ve been hoping to see something like this,” she says.

The post From the Bay of Bengal, a dinoflagellate makes its way to the Smithsonian appeared first on Smithsonian Insider.

The results show mergers of two dense stellar remnants are the likely cause of many of the supernovae that have been used to measure the accelerated expansion of the universe.

The post Mergers of dense stellar remnants are likely trigger for many supernovae appeared first on Smithsonian Insider.

Based on decades of cutting-edge research, the 15,000-square-foot Hall of Human Origins offers visitors an immersive, interactive journey through 6 million years of human evolution spelling out how defining characteristics of the human species have evolved during millions of years in response to a changing world.

The post New Hall of Human Origins points to environmental change as major force in evolution of hominins appeared first on Smithsonian Insider.

About as thick as a standard dictionary, this turtle’s shell may have warded off attacks by the Titanoboa, thought to have been the world’s biggest snake, and by other, crocodile-like creatures living in its neighborhood 60 million years ago.

The post Newly discovered prehistoric turtle co-existed with world’s biggest snake appeared first on Smithsonian Insider.

When it comes to brains, is bigger better? Can the tiny brain of a newly hatched spiderling handle problems as adeptly as the brain of a larger adult spider?

The post Tiny, new brains prove just as adept as large, mature brains among tropical orb-web spiders appeared first on Smithsonian Insider.

The Smithsonian Astrophysical Observatory is a major partner in the Atmospheric Imaging Assembly, which is a group of four telescopes on NASA's Solar Dynamics Observatory that photograph the sun in 10 different wavelength bands, or colors, once every 10 seconds.

The post NASA’s new eye on the sun delivers stunning images appeared first on Smithsonian Insider.

Describing a species is a serious undertaking. In the case of T. acutus, Coats and his collaborators documented its microscopic life cycle, conducted extensive DNA analysis and unearthed scientific papers dating back to 1873—when parasitic dinoflagellates were first noted by German scientist Ernst Haeckel.

The post Introducing the parasitic dinoflagellate: Tintinnophagus acutus appeared first on Smithsonian Insider.

Discoveries of three new from species in Panama lead to hope that project researchers can save these animals from a deadly fungus killing frogs worldwide and the fear that many species will go extinct before scientists even know they exist.

The post New frog species pose challenge for conservation project in Panama appeared first on Smithsonian Insider.

Using the ancient magnetic field recorded in these rocks, a Smithsonian research group revealed Santa Marta’s 2,200-kilometer journey from northern Peru to its modern position on the Caribbean coast of Colombia during the past 170 million years.

The post Earth’s highest coastal mountain range moved 1,367 miles in 170 million years appeared first on Smithsonian Insider.

Researchers at the Smithsonian Conservation Biology Institute conducted three different kinds of genetics tests and all yielded the same result—the Galapagos seabirds have been genetically different from the magnificent frigatebirds elsewhere for more than half a million years.

The post Genetic surprise: Magnificent frigatebird living on Galapagos Islands is distinct species appeared first on Smithsonian Insider.

Darwin's bark spider cast giant webs across streams, rivers and lakes, suspending the web’s orb above water and attaching it to plants on each riverbank. Bridgelines of these water-spanning webs have been measured as long as 25 meters.

The post Newly discovered Madagascar spider spins largest, toughest webs on record appeared first on Smithsonian Insider.

To celebrate a cool Halloween creature--bats--we teamed up with the Smithsonian’s Kristofer Helgen, curator of mammals at the National Museum of Natural History. Here, he answers three commonly asked questions about these winged mammals.

The post Smithsonian bat expert Kristofer Helgen answers common questions about bats appeared first on Smithsonian Insider.

Astronomers using NASA's Chandra X-ray Observatory have found evidence of the youngest black hole known to exist in our cosmic neighborhood. The 30-year-old object is a remnant of SN 1979C, a supernova in the galaxy M100 approximately 50 million light years from Earth.

The post Chandra X-ray Observatory finds youngest nearby black hole appeared first on Smithsonian Insider.

Although the La Loma tree frog, Hyloscirtus colymba, is notoriously difficult to care for in captivity, the Panama Amphibian Rescue and Conservation Project is the first to successfully breed this species.

The post National Zoo and partners first to breed critically endangered tree frog appeared first on Smithsonian Insider.

The turkey has become synonymous with Thanksgiving in the United States. But when exactly where turkeys first domesticated? And where? Bruce Smith, senior archeologist at the Smithsonian’s National Museum of Natural History has the answers.

The post Turkey’s trip to table: Domesticating North America’s largest fowl appeared first on Smithsonian Insider.