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

Many biologists are now routinely seeking to determine the three-dimensional structures of their proteins of choice, illustrating the importance of this knowledge, but also of the simplification and streamlining of structure-determination processes. Despite the fact that most software packages offer simple pipelines, for the non-expert navigating the outputs and understanding the key aspects can be daunting. Here, the structure determination of the type IV pili (TFP) protein PilA1 from Clostridioides difficile is used to illustrate the different steps involved, the key decision criteria and important considerations when using the most common pipelines and software. Molecular-replacement pipelines within CCP4i2 are presented to illustrate the more commonly used processes. Previous knowledge of the biology and structure of TFP pilins, particularly the presence of a long, N-terminal α-helix required for pilus formation, allowed informed decisions to be made during the structure-determination strategy. The PilA1 structure was finally successfully determined using ARCIMBOLDO and the ab initio MR strategy used is described.

Confidence maps provide complementary information for interpreting cryo-EM densities as they indicate statistical significance with respect to background noise. They can be thresholded by specifying the expected false-discovery rate (FDR), and the displayed volume shows the parts of the map that have the corresponding level of significance. Here, the basic statistical concepts of confidence maps are reviewed and practical guidance is provided for their interpretation and usage inside the CCP-EM suite. Limitations of the approach are discussed and extensions towards other error criteria such as the family-wise error rate are presented. The observed map features can be rendered at a common isosurface threshold, which is particularly beneficial for the interpretation of weak and noisy densities. In the current article, a practical guide is provided to the recommended usage of confidence maps.

Multi-slice simulations of electron diffraction by three-dimensional protein crystals have indicated that structure solution would be severely impeded by dynamical diffraction, especially when crystals are more than a few unit cells thick. In practice, however, dynamical diffraction turned out to be less of a problem than anticipated on the basis of these simulations. Here it is shown that two scattering phenomena, which are usually omitted from multi-slice simulations, reduce the dynamical effect: solvent scattering reduces the phase differences within the exit beam and inelastic scattering followed by elastic scattering results in diffusion of dynamical scattering out of Bragg peaks. Thus, these independent phenomena provide potential reasons for the apparent discrepancy between theory and practice in protein electron crystallography.

A tandem-double-slit optical system was constructed to evaluate the practical beam emittance of undulator radiation. The optical system was a combination of an upstream slit (S1) and downstream slit (S2) aligned on the optical axis with an appropriate separation. The intensity distribution after the double slits, I(x1, x2), was measured by scanning S1 and S2 in the horizontal direction. Coordinates having 1/sqrt e intensity were extracted from I(x1, x2), whose contour provided the standard deviation ellipse in the x1–x2 space. I(x1, x2) was converted to the corresponding distribution in the phase space, I(x1, x1'). The horizontal beam emittance was evaluated to be 3.1 nm rad, which was larger than the value of 2.4 nm rad estimated by using ray-tracing. It was found that the increase was mainly due to an increase in beam divergence rather than size.

Enhancement of X-ray excited optical luminescence in a 100 µm-thick diamond plate by introduction of defect states via electron beam irradiation and subsequent high-temperature annealing is demonstrated. The resulting X-ray transmission-mode scintillator features a linear response to incident photon flux in the range 7.6 × 108 to 1.26 × 1012 photons s−1 mm−2 for hard X-rays (15.9 keV) using exposure times from 0.01 to 5 s. These characteristics enable a real-time transmission-mode imaging of X-ray photon flux density without disruption of X-ray instrument operation.

The Inorganic Crystal Structure Database (ICSD) is the world's largest database of fully evaluated and published crystal structure data, mostly obtained from experimental results. However, the purely experimental approach is no longer the only route to discover new compounds and structures. In the past few decades, numerous computational methods for simulating and predicting structures of inorganic solids have emerged, creating large numbers of theoretical crystal data. In order to take account of these new developments the scope of the ICSD was extended in 2017 to include theoretical structures which are published in peer-reviewed journals. Each theoretical structure has been carefully evaluated, and the resulting CIF has been extended and standardized. Furthermore, a first classification of theoretical data in the ICSD is presented, including additional categories used for comparison of experimental and theoretical information.

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.

Bragg intensities can be used to analyse crystal size distributions in a method called FXD-CSD, which is based on the fast measurement of many Bragg spots using two-dimensional detectors. This work presents the Python-based software and its graphical user interface FXD-CSD-GUI. The GUI enables user-friendly data handling and processing and provides both graphical and numerical crystal size distribution results.

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

This article presents IMSIM, an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. IMSIM implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data-analysis pipelines. Intensities and error estimates of one-dimensional patterns obtained from the radial average of the two-dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, [cm−1]/c[mg ml−1], the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample–detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. IMSIM is available as part of the ATSAS software package (3.0.0) and is freely available for academic use (http://www.embl-hamburg.de/biosaxs/download.html).

This article describes rational strategies for the optimization of crystal growth using precise in situ control of the temperature and chemical composition of the crystallization solution through dialysis, to generate crystals of the specific sizes required for different downstream structure determination approaches.

Dynamical X-ray diffraction simulations of very asymmetric diffraction from single crystals of silicon were made to accompany an experimental rocking-curve topography study reported in a seperate paper. Effects on rocking curves were found and are reported. The development of Uragami [(1969), J. Phys. Soc. Jpn, 27, 147–154] for Takagi–Taupin simulations was followed and applied to the case of both convex and concave surface undulations.

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

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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The Smithsonian Tropical Research Institute in Panama was recently given a collection of more than 25,000 different pollen grains and spores, each mounted on a microscope slide and labeled according to the plant that produced it. “The collection is worldwide in coverage with an emphasis on plants of the Americas,” explains collection donor Alan Graham, professor emeritus at Kent State University and curator at the Missouri Botanical Garden.

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In southeastern Greenland, two rivers of ice named Helheim and Kangerdlugssuaq flow in spurts and starts toward the coast. They are much like any other […]

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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 […]

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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!

The post Laboratory tests reveal precise way to measure vertical lift in bumblebees and other small insects and birds 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’s National Zoo recently acquired Japanese giant salamanders given to the Zoo by the City of Hiroshima Asa Zoological Park. This donation will be the foundation of a new long-term breeding program in the United States and may play an important role in saving amphibians around the globe.

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The Smithsonian’s National Zoo celebrated the completion of Phase I of Elephant Trails, an innovative and expanded home for Asian elephants, on Sept. 2. Phase […]

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On Aug, 31, the Smithsonian’s National Zoo welcomed this year’s second litter of African lion (Panthera leo) cubs. Five-year-old Shera (shown at right) gave birth […]

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Should global warming cause sea levels to rise as predicted in coming decades, thousands of archaeological sites in coastal areas around the world will be lost to erosion. With no hope of saving all of these sites, three archaeologists—Leslie Reeder of Southern Methodist University, Jon Erlandson of the University of Oregon and Torben Rick from the Smithsonian's National Museum of Natural History—have issued a call to action for scientists to assess the sites most at risk around the world.

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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.

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Smithsonian Tropical Research Institute community ecologist Sunshine Van Bael primarily examines the relationship between leaf cutter ants–the world’s first farmers–and the fungi that they cultivate.

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Office of Public Affairs videographers Johnny Gibbons and Brian Ireley recently headed down to the Punta Culebra Nature Center on the edge of Panama City […]

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The awarded film features STRI marine biologist Héctor M. Guzman diving with a group of five whale sharks while traveling in the Tropical Eastern Pacific. In the video, Guzmán tags a radiotransmitter to one of the sharks in order to follow its voyages.

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Evidence for a diversified sea-based economy among North American inhabitants dating from 12,200 to 11,400 years ago is emerging from three sites on California's Channel Islands.

The post New archaeological evidence reveals California’s Channel Islands as North America’s earliest seafaring economy appeared first on Smithsonian Insider.

For more than three decades JoGayle Howard dedicated her life and work to reproducing endangered species.

The post JoGayle Howard, National Zoological Park pioneer in reproductive biology, dies appeared first on Smithsonian Insider.

A remarkable 5,000-year-old deposit of bones representing an entire herd of Persian gazelles recently discovered in northeastern Syria is firm evidence, scientists say, of an ancient hunting practice largely responsible for the near extinction of gazelles in this region today.

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Some--birds called wire-tailed manakins, residents of tropical forests in the Americas--are cooperators as well as competitors. They cooperate, forming alliances for a common cause.

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A new genetic study by a team of Cuban and American researchers confirms that American crocodiles are hybridizing with wild populations of critically endangered Cuban crocodiles, which may cause a population decline of this species found only in the Cuban Archipelago.

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The far-out planet, named 55 Cancri e, is twice as big as Earth and nearly nine times more massive. It is most likely composed of rocky material, similar to Earth, supplemented with light elements such as water and hydrogen gas. Scientists estimate the planet’s surface is much hotter than ours: close to 2,700 degrees Celsius.

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Depending on where the fish disperse from, the use of ‘stepping stones', flotsam or simply being an adult can help in the journey to find a new home.

The post Ability to raft with flotsam and use non-reef habitats helps tropical fish journey to new places, study finds appeared first on Smithsonian Insider.

The Smithsonian Tropical Research Institute has released the first completely portable bilingual species identification guide for the shore fishes of the tropical Eastern Pacific as a free iPhone application.

The post First fish App from the Smithsonian free on iTunes. “The Smithsonian Guide to the Shore Fishes of the Tropical Eastern Pacific” appeared first on Smithsonian Insider.

The scientists made the spiders exercise by irritating them with a small paint brush and causing them to move around until they became exhausted. Spiders from the group with palps removed were able to travel 300 percent further than spiders with their palps intact.

The post Weight of genitals reduces physical endurance in male orb web spiders, researchers find appeared first on Smithsonian Insider.

By attaching tiny radio transmitters to more than 400 seeds, Patrick Jansen, scientist at the Smithsonian Tropical Research Institute and Wageningen University, and his colleagues found that 85 percent of the seeds were buried in caches by agoutis, common, house cat-sized rodents in tropical lowlands.

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Almost half of the tropical forest reserves examined in a new study are ineffective, researchers say.

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What scientists found was that the domestic turkey that ends up on the dinner table exhibits less genetic variation than its ancestral wild counterparts, which were first domesticated in 800 B.C..

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A specimen recently pulled from deep in the southwest Atlantic may represent a new species of squid, say scientist who have studied the animal’s unusual morphology. But then again, it may not…

The post As they grow some squid change dramatically, making scientists cautious about naming new species appeared first on Smithsonian Insider.

Astronomers have discovered that one well-known elliptical galaxy has a split personality. Centaurus A is hiding a gassy spiral in its center.

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The Smithsonian Astrophysical Observatory has been awarded a NASA project to build the Tropospheric Emissions: Monitoring of Pollution (TEMPO) instrument. TEMPO will measure North American air pollution, from Mexico City to the Canadian tar/oil sands, and from the Atlantic to the Pacific, hourly and at high spatial resolution.

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Using echolocation alone the bats found, identified and captured insects perched motionless and silent on the leaves of plants.

The post Common tropical bat uses echolocation with precision previously considered impossible, new experiments reveal appeared first on Smithsonian Insider.

Recent spectroscopic analysis of macaroni penguin (Eudyptes chrysolophus) crest feathers and king penguin (Aptenodytes patagonicus) neck feathers have shown they contain a yellow pigment that […]

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The Sun’s outer atmosphere, or corona, has posed an enduring mystery. Why is it so hot? The Sun’s visible surface is only 10,000 degrees Fahrenheit, […]

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Found worldwide in tropical and subtropical seas and oceans, Dolabrifera dolabrifera is a species of sea hare, a marine gastropod mollusk in the family Aplysiidae. […]

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The world of astronomy has changed. An astronomer used to have to travel to a remote location and endure long, cold nights, patiently guiding a […]

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