Although the success of molecular-replacement techniques requires the solution of a six-dimensional problem, this is often subdivided into two three-dimensional problems. REMO09 is one of the programs which have adopted this approach. It has been revisited in the light of a new probabilistic approach which is able to directly derive conditional distribution functions without passing through a previous calculation of the joint probability distributions. The conditional distributions take into account various types of prior information: in the rotation step the prior information may concern a non-oriented model molecule alone or together with one or more located model molecules. The formulae thus obtained are used to derive figures of merit for recognizing the correct orientation in the rotation step and the correct location in the translation step. The phases obtained by this new version of REMO09 are used as a starting point for a pipeline which in its first step extends and refines the molecular-replacement phases, and in its second step creates the final electron-density map which is automatically interpreted by CAB, an automatic model-building program for proteins and DNA/RNA structures.

Good prior estimates of the effective root-mean-square deviation (r.m.s.d.) between the atomic coordinates of the model and the target optimize the signal in molecular replacement, thereby increasing the success rate in difficult cases. Previous studies using protein structures solved by X-ray crystallography as models showed that optimal error estimates (refined after structure solution) were correlated with the sequence identity between the model and target, and with the number of residues in the model. Here, this work has been extended to find additional correlations between parameters of the model and the target and hence improved prior estimates of the coordinate error. Using a graph database, a curated set of 6030 molecular-replacement calculations using models that had been solved by X-ray crystallography was analysed to consider about 120 model and target parameters. Improved estimates were achieved by replacing the sequence identity with the Gonnet score for sequence similarity, as well as by considering the resolution of the target structure and the MolProbity score of the model. This approach was extended by analysing 12 610 additional molecular-replacement calculations where the model was determined by NMR. The median r.m.s.d. between pairs of models in an ensemble was found to be correlated with the estimated r.m.s.d. to the target. For models solved by NMR, the overall coordinate error estimates were larger than for structures determined by X-ray crystallography, and were more highly correlated with the number of residues.

Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β-sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log-likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary-structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute-force approach through side-chain building and refinement. Scoring the refined models through their LLG in Phaser may allow discrimination of the correct sequence or filter the best partial structures for further density modification and autotracing. The default limits for the number of models to pursue are hardware dependent. In its most economic implementation, suitable for a single laptop, the main-chain trace is extended as polyserine rather than trialling models with different sequence assignments, which requires a grid or multicore machine. SEQUENCE SLIDER has been instrumental in solving two novel structures: that of MltC from 2.7 Å resolution data and that of a pneumococcal lipoprotein with 638 residues and 35% solvent content.

The performance of automated protein model building usually decreases with resolution, mainly owing to the lower information content of the experimental data. This calls for a more elaborate use of the available structural information about macromolecules. Here, a new method is presented that uses structural homologues to improve the quality of protein models automatically constructed using ARP/wARP. The method uses local structural similarity between deposited models and the model being built, and results in longer main-chain fragments that in turn can be more reliably docked to the protein sequence. The application of the homology-based model extension method to the example of a CFA synthase at 2.7 Å resolution resulted in a more complete model with almost all of the residues correctly built and docked to the sequence. The method was also evaluated on 1493 molecular-replacement solutions at a resolution of 4.0 Å and better that were submitted to the ARP/wARP web service for model building. A significant improvement in the completeness and sequence coverage of the built models has been observed.

This paper discusses the full structural solution of the hybrid perovskite formamidinium lead tribromide (FAPbBr3) and its temperature-dependent phase transitions in the range from 3 K to 300 K using neutron powder diffraction and synchrotron X-ray diffraction. Special emphasis is put on the influence of deuteration on formamidinium, its position in the unit cell and disordering in comparison to fully hydrogenated FAPbBr3. The temperature-dependent measurements show that deuteration critically influences the crystal structures, i.e. results in partially-ordered temperature-dependent structural modifications in which two symmetry-independent molecule positions with additional dislocation of the molecular centre atom and molecular angle inclinations are present.

In recent years, there have been numerous efforts worldwide to develop the synchrotron X-ray scanning tunneling microscopy (SX-STM) technique. Here, the inauguration of XTIP, the world's first beamline fully dedicated to SX-STM, is reported. The XTIP beamline is located at Sector 4 of the Advanced Photon Source at Argonne National Laboratory. It features an insertion device that can provide left- or right-circular as well as horizontal- and vertical-linear polarization. XTIP delivers monochromatic soft X-rays of between 400 and 1900 eV focused into an environmental enclosure that houses the endstation instrument. This article discusses the beamline system design and its performance.

The room-temperature experiment has been revisited for macromolecular crystallography. Despite being limited by radiation damage, such experiments reveal structural differences depending on temperature, and it is expected that they will be able to probe structures that are physiologically alive. For such experiments, the humid-air and glue-coating (HAG) method for humidity-controlled experiments is proposed. The HAG method improves the stability of most crystals in capillary-free experiments and is applicable at both cryogenic and ambient temperatures. To expand the thermal versatility of the HAG method, a new humidifier and a protein-crystal-handling workbench have been developed. The devices provide temperatures down to 4°C and successfully maintain growth at that temperature of bovine cytochrome c oxidase crystals, which are highly sensitive to temperature variation. Hence, the humidifier and protein-crystal-handling workbench have proved useful for temperature-sensitive samples and will help reveal temperature-dependent variations in protein structures.

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.

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.

A new temperature-controllable humidifier for X-ray diffraction has been developed. It is shown that the humidifier can successfully maintain protein crystal growth at a temperature lower than room temperature.

An energy resolution of <10 µeV for the measurement of phonon energy change is achieved with the inelastic neutron spin echo technique on a conventional neutron triple-axis spectrometer.

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.

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.

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.

Take to the water with this behind-the-scenes video about Maryland blue crab research at the Smithsonian's Environmental Research Center. Fisheries Ecologist Eric Johnson takes viewers on a journey along the Rhode River to show how scientists tag and monitor Maryland blue crabs in the Chesapeake Bay watershed.

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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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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.

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In a new paper, Harvard-Smithsonian Center for Astrophysics astronomer Hagai Perets studies the role of binary planetesimals--clumps that orbit each other and jointly mature via three basic processes.

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“Our results support the idea that environmental conditions on tropical non-breeding areas can influence the departure time for spring migration,” said Colin Studds, a postdoctoral fellow at the Smithsonian Conservation Biology Institute's Migratory Bird Center and lead author of the study.

The post Smithsonian scientists find declining rainfall is a major influence for migrating birds appeared first on Smithsonian Insider.

Small tissue samples collected from 238 wild turtles at 15 different locations across their range in Southern Mexico, Belize and Guatemala revealed a “surprising lack” of genetic structure, the scientists write in a recent paper in the journal Conservation Genetics.

The post Endangered river turtle’s genes reveal ancient influence of Maya Indians appeared first on Smithsonian Insider.

Now, for the first time scientists at the Smithsonian’s Museum Conservation Institute have developed a fast and reliable method to date silk.

The post New technique for dating silk developed by Smithsonian conservation team appeared first on Smithsonian Insider.

History and geology, not current ecology, are likely what has made tropical forests so variable from site to site.

The post What makes rainforests unique? History, not ecology. appeared first on Smithsonian Insider.

In honor of Halloween, Michael Miller, keeper in the National Zoological Park's Invertebrate Exhibit, shares a few of his favorite "strange-but-true" spider facts.

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Today, Marra is helping launch an Animal Mortality Monitoring Program in Africa intended to serve as an early warning system for emerging infectious diseases that can pass from animal populations into the human population.

The post Uganda park rangers with cell phones may help stop next world influenza epidemic appeared first on Smithsonian Insider.

Smithsonian astronomers have joined their colleagues from other observatories in a daring new venture: to photograph the giant black hole at the heart of our Milky Way galaxy.

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Just a few towering white fir, sugar pine and incense cedars per acre at Yosemite National Park are disproportionately responsible for photosynthesis, converting carbon dioxide into plant tissue and sequestering that carbon in the forest, sometimes for centuries,

The post Heavyweight trees are forest champs at sequestering carbon appeared first on Smithsonian Insider.

To celebrate the 10th anniversary of researchers producing the first complete human genome sequence — the genetic blueprint of the human body — the Smithsonian’s National Museum of Natural History, will open a new high-tech, high-intensity exhibition in 2013.

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Coral reefs worldwide are being destroyed by changes in ocean temperature and chemistry faster than at any time since the last reef crisis 55 million years ago, thousands of marine scientists warned from the International Coral Reef Symposium in Cairns, Australia.

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“Ignition Sequence,” 1968, Vincent Cavallaro, oil on canvas. The power of the ignition and launch sequence of a NASA rocket is portrayed in an abstract […]

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Archaeologists working at the Smithsonian Tropical Research Institute in Panama have discovered a cluster of 12 unusual stones in the back of a small, prehistoric rock-shelter near the town of Boquete.

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There is little doubt that human activity is affecting planet Earth, but just how much? And is it all negative? Rick Potts is the director […]

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For scientists who study non-insect invertebrates, the sheer diversity of these odd and fascinating creatures is both intoxicating and daunting. Occupying niches in habitats the […]

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Parents normally feel the need to provide well for their kids. For humans, that number of offspring is usually in the single digits, but a […]

The post The secret formula to feeding 900 babies: Scientists uncover milk composition of naked mole-rat queens appeared first on Smithsonian Insider.

A new study of gamma-ray light from the center of our galaxy makes the strongest case to date that some of this emission may arise […]

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John Kovac of the Harvard-­Smithsonian Center for Astrophysics has been named one of Time Magazine’s 100 most influential people. 

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The practice of selectively fishing male blue crabs in the Chesapeake—intended to give females a chance to reproduce—may have a hidden cost. A Bay without […]

The post With too few males, blue crab population may be put at risk appeared first on Smithsonian Insider.

A few images of comet 67P/Churyumov-Gerasimenko just sent back by the European spaceship Rosetta appear to be a snowboarder’s dream: pristine slopes covered in powder. […]

The post Comet probe set to answer ancient question of life on earth appeared first on Smithsonian Insider.

1. Some male spiders just want to be eaten Black widows are known for cannibalizing their mates, but this doesn’t actually happen all the time. […]

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Bright orange with a distinctive call the Panamanian poison dart frog Andinobates geminisae lives in only a small area of the Caribbean Coast of Panama. […]

The post In modern amphibian “ark,” new species added with due diligence appeared first on Smithsonian Insider.

Eaten raw and thinly sliced, the dark-red belly meat of the Pacific bluefin tuna is highly prized—and priced—for its rich oily flavor by sashimi and […]

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A new study published this week in the Proceedings of the Royal Society by scientists at the Smithsonian Conservation Biology Institute (SCBI) found unique communities […]

The post Golden Frogs with Unique Skin Microbes Survive Frog-Killing Fungus appeared first on Smithsonian Insider.

Stars form when gravity pulls together material within giant clouds of gas and dust. But gravity isn’t the only force at work. Both turbulence and […]

The post As Stars Form, Magnetic Fields Influence Regions Big and Small appeared first on Smithsonian Insider.

Who: Wheelerodemus muhlenbergiae What: A newly discovered species of plant eating bug belonging to the family Blissidae, members of which are found worldwide. W. muhlenbergiae […]

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Bei Bei, Bao Bao, Tian Tian. Many people recognize the names of the giant pandas that reside at the Smithsonian’s National Zoo. Yet Juan Rodriguez […]

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The results are in, 2016 is going to be a good year for blue crabs in the Chesapeake Bay. An iconic figure embedded in the […]

The post Smithsonian Expert Urges Caution, Patience on Blue Crab Recovery appeared first on Smithsonian Insider.

When is a blue bird not blue? The answer to this question is always. There actually is no such thing as a blue bird. To find […]

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In 1935, 101 cane toads from Hawaii were set loose in Australia to help control beetles that were decimating the Australian sugar crop. But instead […]

The post Discovery: Australia’s invasive cane toads modify their bodies to conquer new territory faster appeared first on Smithsonian Insider.

Fetching close to $1,500 per pound, ivory ranks fourth in black-market traded items just behind illegal drugs, weapons, and humans. Governments across the globe are […]

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