ir Throughput and resolution with a next-generation direct electron detector By scripts.iucr.org Published On :: 2019-10-24 Direct electron detectors (DEDs) have revolutionized cryo-electron microscopy (cryo-EM) by facilitating the correction of beam-induced motion and radiation damage, and also by providing high-resolution image capture. A new-generation DED, the DE64, has been developed by Direct Electron that has good performance in both integrating and counting modes. The camera has been characterized in both modes in terms of image quality, throughput and resolution of cryo-EM reconstructions. The modulation transfer function, noise power spectrum and detective quantum efficiency (DQE) were determined for both modes, as well as the number of images per unit time. Although the DQE for counting mode was superior to that for integrating mode, the data-collection throughput for this mode was more than ten times slower. Since throughput and resolution are related in single-particle cryo-EM, data for apoferritin were collected and reconstructed using integrating mode, integrating mode in conjunction with a Volta phase plate (VPP) and counting mode. Only the counting-mode data resulted in a better than 3 Å resolution reconstruction with similar numbers of particles, and this increased performance could not be compensated for by the increased throughput of integrating mode or by the increased low-frequency contrast of integrating mode with the VPP. These data show that the superior image quality provided by counting mode is more important for high-resolution cryo-EM reconstructions than the superior throughput of integrating mode. Full Article text
ir A fixed-target platform for serial femtosecond crystallography in a hydrated environment By scripts.iucr.org Published On :: 2020-01-01 For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering. Full Article text
ir The resolution revolution in cryoEM requires high-quality sample preparation: a rapid pipeline to a high-resolution map of yeast fatty acid synthase By scripts.iucr.org Published On :: 2020-01-25 Single-particle electron cryo-microscopy (cryoEM) has undergone a `resolution revolution' that makes it possible to characterize megadalton (MDa) complexes at atomic resolution without crystals. To fully exploit the new opportunities in molecular microscopy, new procedures for the cloning, expression and purification of macromolecular complexes need to be explored. Macromolecular assemblies are often unstable, and invasive construct design or inadequate purification conditions and sample-preparation methods can result in disassembly or denaturation. The structure of the 2.6 MDa yeast fatty acid synthase (FAS) has been studied by electron microscopy since the 1960s. Here, a new, streamlined protocol for the rapid production of purified yeast FAS for structure determination by high-resolution cryoEM is reported. Together with a companion protocol for preparing cryoEM specimens on a hydrophilized graphene layer, the new protocol yielded a 3.1 Å resolution map of yeast FAS from 15 000 automatically picked particles within a day. The high map quality enabled a complete atomic model of an intact fungal FAS to be built. Full Article text
ir First synthesis of a unique icosahedral phase from the Khatyrka meteorite by shock-recovery experiment By scripts.iucr.org Published On :: 2020-03-26 Icosahedral quasicrystals (i-phases) in the Al–Cu–Fe system are of great interest because of their perfect quasicrystalline structure and natural occurrences in the Khatyrka meteorite. The natural quasicrystal of composition Al62Cu31Fe7, referred to as i-phase II, is unique because it deviates significantly from the stability field of i-phase and has not been synthesized in a laboratory setting to date. Synthetic i-phases formed in shock-recovery experiments present a novel strategy for exploring the stability of new quasicrystal compositions and prove the impact origin of natural quasicrystals. In this study, an Al–Cu–W graded density impactor (GDI, originally manufactured as a ramp-generating impactor but here used as a target) disk was shocked to sample a full range of Al/Cu starting ratios in an Fe-bearing 304 stainless-steel target chamber. In a strongly deformed region of the recovered sample, reactions between the GDI and the steel produced an assemblage of co-existing Al61.5Cu30.3Fe6.8Cr1.4 i-phase II + stolperite (β, AlCu) + khatyrkite (θ, Al2Cu), an exact match to the natural i-phase II assemblage in the meteorite. In a second experiment, the continuous interface between the GDI and steel formed another more Fe-rich quinary i-phase (Al68.6Fe14.5Cu11.2Cr4Ni1.8), together with stolperite and hollisterite (λ, Al13Fe4), which is the expected assemblage at phase equilibrium. This study is the first laboratory reproduction of i-phase II with its natural assemblage. It suggests that the field of thermodynamically stable icosahedrite (Al63Cu24Fe13) could separate into two disconnected fields under shock pressure above 20 GPa, leading to the co-existence of Fe-rich and Fe-poor i-phases like the case in Khatyrka. In light of this, shock-recovery experiments do indeed offer an efficient method of constraining the impact conditions recorded by quasicrystal-bearing meteorite, and exploring formation conditions and mechanisms leading to quasicrystals. Full Article text
ir Expression and interactions of stereochemically active lone pairs and their relation to structural distortions and thermal conductivity By scripts.iucr.org Published On :: 2020-03-31 In chemistry, stereochemically active lone pairs are typically described as an important non-bonding effect, and recent interest has centred on understanding the derived effect of lone pair expression on physical properties such as thermal conductivity. To manipulate such properties, it is essential to understand the conditions that lead to lone pair expression and provide a quantitative chemical description of their identity to allow comparison between systems. Here, density functional theory calculations are used first to establish the presence of stereochemically active lone pairs on antimony in the archetypical chalcogenide MnSb2O4. The lone pairs are formed through a similar mechanism to those in binary post-transition metal compounds in an oxidation state of two less than their main group number [e.g. Pb(II) and Sb(III)], where the degree of orbital interaction (covalency) determines the expression of the lone pair. In MnSb2O4 the Sb lone pairs interact through a void space in the crystal structure, and their their mutual repulsion is minimized by introducing a deflection angle. This angle increases significantly with decreasing Sb—Sb distance introduced by simulating high pressure, thus showing the highly destabilizing nature of the lone pair interactions. Analysis of the chemical bonding in MnSb2O4 shows that it is dominated by polar covalent interactions with significant contributions both from charge accumulation in the bonding regions and from charge transfer. A database search of related ternary chalcogenide structures shows that, for structures with a lone pair (SbX3 units), the degree of lone pair expression is largely determined by whether the antimony–chalcogen units are connected or not, suggesting a cooperative effect. Isolated SbX3 units have larger X—Sb—X bond angles and therefore weaker lone pair expression than connected units. Since increased lone pair expression is equivalent to an increased orbital interaction (covalent bonding), which typically leads to increased heat conduction, this can explain the previously established correlation between larger bond angles and lower thermal conductivity. Thus, it appears that for these chalcogenides, lone pair expression and thermal conductivity may be related through the degree of covalency of the system. Full Article text
ir Crystal structure of the NS3-like helicase from Alongshan virus By scripts.iucr.org Published On :: 2020-04-10 Alongshan virus (ALSV) is an emerging human pathogen that was identified in China and rapidly spread to the European continent in 2019, raising concerns about public health. ALSV belongs to the distinct Jingmenvirus group within the Flaviviridae family with segmented RNA genomes. While segments 2 and 4 of the ALSV genome encode the VP1–VP3 proteins of unknown origin, segments 1 and 3 encode the NS2b–NS3 and NS5 proteins, which are related to Flavivirus nonstructural proteins, suggesting an evolutionary link between segmented and unsegmented viruses within the Flaviviridae family. Here, the enzymatic activity of the ALSV NS3-like helicase (NS3-Hel) was characterized and its crystal structure was determined to 2.9 Å resolution. ALSV NS3-Hel exhibits an ATPase activity that is comparable to those measured for Flavivirus NS3 helicases. The structure of ALSV NS3-Hel exhibits an overall fold similar to those of Flavivirus NS3 helicases. Despite the limited amino-acid sequence identity between ALSV NS3-Hel and Flavivirus NS3 helicases, structural features at the ATPase active site and the RNA-binding groove remain conserved in ALSV NS3-Hel. These findings provide a structural framework for drug design and suggest the possibility of developing a broad-spectrum antiviral drug against both Flavivirus and Jingmenvirus. Full Article text
ir X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein By scripts.iucr.org Published On :: 2019-08-28 The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe–4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer. Full Article text
ir Noncrystallographic symmetry-constrained map obtained by direct density optimization By scripts.iucr.org Published On :: 2020-01-31 Noncrystallographic symmetry (NCS) averaging following molecular-replacement phasing is generally the major technique used to solve a structure with several molecules in one asymmetric unit, such as a spherical icosahedral viral particle. As an alternative method to NCS averaging, a new approach to optimize or to refine the electron density directly under NCS constraints is proposed. This method has the same effect as the conventional NCS-averaging method but does not include the process of Fourier synthesis to generate the electron density from amplitudes and the corresponding phases. It has great merit for the solution of structures with limited data that are either twinned or incomplete at low resolution. This method was applied to the case of the T = 1 shell-domain subviral particle of Penaeus vannamei nodavirus with data affected by twinning using the REFMAC5 refinement software. Full Article text
ir The crystal structure of the heme d1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo By scripts.iucr.org Published On :: 2020-03-25 Monoheme c-type cytochromes are important electron transporters in all domains of life. They possess a common fold hallmarked by three α-helices that surround a covalently attached heme. An intriguing feature of many monoheme c-type cytochromes is their capacity to form oligomers by exchanging at least one of their α-helices, which is often referred to as 3D domain swapping. Here, the crystal structure of NirC, a c-type cytochrome co-encoded with other proteins involved in nitrite reduction by the opportunistic pathogen Pseudomonas aeruginosa, has been determined. The crystals diffracted anisotropically to a maximum resolution of 2.12 Å (spherical resolution of 2.83 Å) and initial phases were obtained by Fe-SAD phasing, revealing the presence of 11 NirC chains in the asymmetric unit. Surprisingly, these protomers arrange into one monomer and two different types of 3D domain-swapped dimers, one of which shows pronounced asymmetry. While the simultaneous observation of monomers and dimers probably reflects the interplay between the high protein concentration required for crystallization and the structural plasticity of monoheme c-type cytochromes, the identification of conserved structural motifs in the monomer together with a comparison with similar proteins may offer new leads to unravel the unknown function of NirC. Full Article text
ir Structural elucidation of triclinic and monoclinic SFCA-III – killing two birds with one stone By scripts.iucr.org Published On :: 2019-11-20 A part of the system CaO-SiO2–Al2O3–Fe2O3–MgO which is of relevance to iron-ore sintering has been studied in detail. For a bulk composition corresponding to 10.45 wt% CaO, 5.49 wt% MgO, 69.15 wt% Fe2O3, 13.37 wt% Al2O3 and 1.55 wt% SiO2 synthesis runs have been performed in air in the range between 1100 and 1300°C. Products have been characterized using reflected-light microscopy, electron microprobe analysis and diffraction techniques. At 1250°C, an almost phase-pure material with composition Ca2.99Mg2.67Fe3+14.58Fe2+0.77Al4.56Si0.43O36 has been obtained. The compound corresponds to the first Si-containing representative of the M14+6nO20+8n polysomatic series of so-called SFCA phases (Silico-Ferrites of Calcium and Aluminum) with n = 2 and is denoted as SFCA-III. Single-crystal diffraction investigations using synchrotron radiation at the X06DA beamline of the Swiss Light Source revealed that the chemically homogenous sample contained both a triclinic and monoclinic polytype. Basic crystallographic data are as follows: triclinic form: a = 10.3279 (2) Å, b = 10.4340 (2) Å, c = 14.3794 (2) Å, α = 93.4888 (12)°, β = 107.3209 (14)° and γ = 109.6626 (14)°, V = 1370.49 (5) Å3, Z = 2, space group P{overline 1}; monoclinic form: a = 10.3277 (2) Å, b = 27.0134 (4) Å, c = 10.4344 (2) Å, β = 109.668 (2)°, V = 2741.22 (9) Å3, Z = 4, space group P21/n. Structure determination of both modifications was successful using diffraction data from the same allotwinned crystal. A description of the observed polytypism within the framework of OD-theory is presented. Triclinic and monoclinic SFCA-III actually correspond to the two possible maximum degree of order structures based on OD-layers containing three spinel (S) and one pyroxene (P) modules (〈S3P〉). The existence of SFCA-III in industrial iron-ore sinters has yet to be confirmed. Polytypism is likely to occur in other SFCA-members (SFCA, SFCA-I) relevant to sintering as well, but has so far been neglected in the characterization of industrial samples. Our results shed light on this phenomenon and may therefore be also helpful for better interpretation of the powder diffraction patterns that are used for phase analysis of iron-ore sinters. Full Article text
ir XTIP – the world's first beamline dedicated to the synchrotron X-ray scanning tunneling microscopy technique By scripts.iucr.org Published On :: 2020-04-14 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. Full Article text
ir Foreword to the special virtual issue on X-ray free-electron lasers By scripts.iucr.org Published On :: 2020-05-01 Full Article text
ir A temperature-controlled cold-gas humidifier and its application to protein crystals with the humid-air and glue-coating method By scripts.iucr.org Published On :: 2019-06-14 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. Full Article text
ir POWGEN: rebuild of a third-generation powder diffractometer at the Spallation Neutron Source By scripts.iucr.org Published On :: 2019-10-01 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. Full Article text
ir Direct protein crystallization on ultrathin membranes for diffraction measurements at X-ray free-electron lasers. Corrigendum By scripts.iucr.org Published On :: 2019-10-17 Errors in the article by Opara, Martiel, Arnold, Braun, Stahlberg, Makita, David & Padeste [J. Appl. Cryst. (2017), 50, 909–918] are corrected. Full Article text
ir Real- and Q-space travelling: multi-dimensional distribution maps of crystal-lattice strain (∊044) and tilt of suspended monolithic silicon nanowire structures By scripts.iucr.org Published On :: 2020-02-01 Silicon nanowire-based sensors find many applications in micro- and nano-electromechanical systems, thanks to their unique characteristics of flexibility and strength that emerge at the nanoscale. This work is the first study of this class of micro- and nano-fabricated silicon-based structures adopting the scanning X-ray diffraction microscopy technique for mapping the in-plane crystalline strain (∊044) and tilt of a device which includes pillars with suspended nanowires on a substrate. It is shown how the micro- and nanostructures of this new type of nanowire system are influenced by critical steps of the fabrication process, such as electron-beam lithography and deep reactive ion etching. X-ray analysis performed on the 044 reflection shows a very low level of lattice strain (<0.00025 Δd/d) but a significant degree of lattice tilt (up to 0.214°). This work imparts new insights into the crystal structure of micro- and nanomaterial-based sensors, and their relationship with critical steps of the fabrication process. Full Article text
ir The nondestructive measurement of strain distributions in air plasma sprayed thermal barrier coatings as a function of depth from entire Debye–Scherrer rings By scripts.iucr.org Published On :: 2020-02-01 The residual strain distribution has been measured as a function of depth in both top coat and bond coat in as-received and heat-treated air plasma sprayed thermal barrier coating samples. High-energy synchrotron X-ray beams were used in transmission to produce full Debye–Scherrer rings whose non-circular aspect ratio gave the in-plane and out-of-plane strains far more efficiently than the sin2ψ method. The residual strain in the bond coat is found to be tensile and the strain in the β phase of the as-received sample was measured. The residual strains observed in the top coat were generally compressive (increasing towards the interface), with two kinds of nonlinear trend. These was a `jump' feature near the interface, and in some cases there was another `jump' feature near the surface. It is shown how these trend differences can be correlated to cracks in the coating. Full Article text
ir Structure analysis of supported disordered molybdenum oxides using pair distribution function analysis and automated cluster modelling By scripts.iucr.org Published On :: 2020-02-01 Molybdenum oxides and sulfides on various low-cost high-surface-area supports are excellent catalysts for several industrially relevant reactions. The surface layer structure of these materials is, however, difficult to characterize due to small and disordered MoOx domains. Here, it is shown how X-ray total scattering can be applied to gain insights into the structure through differential pair distribution function (d-PDF) analysis, where the scattering signal from the support material is subtracted to obtain structural information on the supported structure. MoOx catalysts supported on alumina nanoparticles and on zeolites are investigated, and it is shown that the structure of the hydrated molybdenum oxide layer is closely related to that of disordered and polydisperse polyoxometalates. By analysing the PDFs with a large number of automatically generated cluster structures, which are constructed in an iterative manner from known polyoxometalate clusters, information is derived on the structural motifs in supported MoOx. Full Article text
ir A temperature-controlled cold-gas humidifier and its application to protein crystals with the humid-air and glue-coating method By journals.iucr.org Published On :: 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. Full Article text
ir Disorder in La1−xBa1+xGaO4−x/2 ionic conductor: resolving the pair distribution function through insight from first-principles modeling By journals.iucr.org Published On :: Ba excess in LaBaGaO4 triggers ionic conductivity together with structural disorder. A direct correlation is found between the density functional theory model energy and the pair distribution function fit residual. Full Article text
ir Nanometre-sized droplets from a gas dynamic virtual nozzle By journals.iucr.org Published On :: This work describes a method to characterize the size distribution of individual aqueous droplets in a high-density and polydisperse aerosol. It is shown that droplets smaller than 120 nm can be generated by purely mechanical means using a gas dynamic virtual nozzle, and theoretical models are provided for the different flow regimes investigated. Full Article text
ir Handbook of Industrial Crystallization. Third edition. Edited by Allan S. Myerson, Deniz Erdemir and Alfred Y. Lee. Cambridge University Press, 2019. Pp. 538. Price GBP 145 (hardcover). ISBN 9780521196185. By journals.iucr.org Published On :: Book review Full Article text
ir Exact and fast calculation of the X-ray pair distribution function By journals.iucr.org Published On :: 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. Full Article text
ir sasPDF: pair distribution function analysis of nanoparticle assemblies from small-angle scattering data By journals.iucr.org Published On :: The sasPDF method, an extension of the atomic pair distribution function (PDF) analysis to the small-angle scattering (SAS) regime, is presented. The method is applied to characterize the structure of nanoparticle assemblies with different levels of structural order. Full Article text
ir GIWAXS-SIIRkit: Scattering Intensity, Indexing, and Refraction Calculation Toolkit for Grazing Incidence Wide Angle X-ray Scattering of Organic Materials By journals.iucr.org Published On :: 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. Full Article text
ir Orientational disorder of monomethyl-quinacridone investigated by Rietveld refinement, structure refinement to the pair distribution function and lattice-energy minimizations By scripts.iucr.org Published On :: 2020-05-08 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. Full Article text
ir Crystallization of chiral molecular compounds: what can be learned from the Cambridge Structural Database? By scripts.iucr.org Published On :: 2020-04-10 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. Full Article text
ir Crystallization of chiral molecular compounds: what can be learned from the Cambridge Structural Database? By journals.iucr.org Published On :: A study on chiral monomolecular compound structures found in the Cambridge Structural Database is presented. Full Article text
ir Orientational disorder of monomethyl-quinacridone investigated by Rietveld refinement, structure refinement to the pair-distribution function and lattice-energy minimizations By journals.iucr.org Published On :: 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. Full Article text
ir Structure of the Prx6-subfamily 1-Cys peroxiredoxin from Sulfolobus islandicus By scripts.iucr.org Published On :: 2019-05-13 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. Full Article text
ir Salad science: Coaxing caterpillars to reveal the secrets of their leafy desires By insider.si.edu Published On :: Tue, 15 Sep 2009 17:50:07 +0000 Testing caterpillars’ taste buds is no simple task. Just like your local salad bar, plants in the wild come in different shapes, textures and flavors. Herbivores rely on each of these cues to tell them what to eat. Deciphering this code is Lind’s task. He’s examining 40 different plant species – half invasive, half native. The post Salad science: Coaxing caterpillars to reveal the secrets of their leafy desires appeared first on Smithsonian Insider. Full Article Research News Science & Nature conservation biology Smithsonian Environmental Research Center
ir The Smithsonian’s National Air and Space Museum opens new Public Observatory on the Mall in Washington, D.C. By insider.si.edu Published On :: Wed, 30 Sep 2009 17:27:39 +0000 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. Full Article Space astronomy National Air and Space Museum
ir Video: Common birds in Washington, D.C. are helping Smithsonian scientists track intensity of the West Nile Virus By insider.si.edu Published On :: Wed, 07 Oct 2009 13:46:11 +0000 Scientists from the Smithsonian Migratory Bird Center at the National Zoo have taken blood samples from thousands of birds and mosquitoes in an effort to track the progress of the West Nile Virus in the eastern United States. Come along in this video as Smithsonian scientists net birds living in downtown Washington, D.C., extract small amounts of blood, and then release them back into the "wild." The post Video: Common birds in Washington, D.C. are helping Smithsonian scientists track intensity of the West Nile Virus appeared first on Smithsonian Insider. Full Article Research News Science & Nature birds Migratory Bird Center Smithsonian's National Zoo
ir In face of crisis, National Zoo to start captive population of Virginia big-eared bats By insider.si.edu Published On :: Mon, 26 Oct 2009 18:20:18 +0000 The National Zoo has been awarded a grant from the U.S. Fish and Wildlife Service to establish a captive population of the Virginia big-eared bat at the National Zoo’s Conservation & Research Center near Front Royal, Va. Only 15,000 Virginia big-eared bats remain living in caves in West Virginia, Virginia, Kentucky and North Carolina, and these are threatened by the white-nose syndrome. The post In face of crisis, National Zoo to start captive population of Virginia big-eared bats appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature bats conservation conservation biology endangered species mammals Smithsonian's National Zoo
ir Dennis Kelly Named Director of the Smithsonian’s National Zoo By insider.si.edu Published On :: Fri, 11 Dec 2009 15:00:57 +0000 Dennis W. Kelly has been named director of the Smithsonian’s National Zoo in Washington, D.C., effective Feb. 15, 2010. The post Dennis Kelly Named Director of the Smithsonian’s National Zoo appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature Smithsonian's National Zoo
ir Strawberry dart frogs bred at National Zoo for first time in Zoo’s history By insider.si.edu Published On :: Wed, 06 Jan 2010 13:00:14 +0000 For the first time in its history, the National Zoo has bred strawberry dart frogs (Oophaga pumilio), which are known primarily for their vibrant colors and poisonous skin. These frogs also stand out among others because of their dedication to their young as they undergo metamorphosis from egg to tadpole to frog. The post Strawberry dart frogs bred at National Zoo for first time in Zoo’s history appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature amphibian chytrid fungus conservation biology endangered species frogs Smithsonian's National Zoo
ir For first time, scientists prove locusts use vision to place their legs when walking By insider.si.edu Published On :: Thu, 14 Jan 2010 18:35:09 +0000 In their laboratory, scientists from the University of Cambridge, the University of Southampton and the Smithsonian Tropical Research Institute in Panama, observed as a number of adult locusts walked along a horizontal ladder. After covering the right or left eye of an insect, the scientists observed a significant increase in the error rate of rungs missed by the front leg on the side of the covered eye. The post For first time, scientists prove locusts use vision to place their legs when walking appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature insects Tropical Research Institute
ir Laboratory tests reveal precise way to measure vertical lift in bumblebees and other small insects and birds By insider.si.edu Published On :: Thu, 28 Jan 2010 20:01:27 +0000 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. Full Article Animals Research News Science & Nature animal flight bees birds insects Tropical Research Institute
ir Captive colony of Virginia big-eared bats providing valuable lessons in battle against deadly white-nose syndrome By insider.si.edu Published On :: Sat, 06 Mar 2010 10:15:28 +0000 Eleven bats remain in the National Zoo’s colony. The initial challenge the team faced was how to feed the animals. Virginia big-eared bats, which are a subspecies of the Townsend’s big-eared bat (Corynorhinuss townsendii), eat while flying. The post Captive colony of Virginia big-eared bats providing valuable lessons in battle against deadly white-nose syndrome appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature bats biodiversity conservation conservation biology endangered species extinction Smithsonian's National Zoo
ir New Hall of Human Origins points to environmental change as major force in evolution of hominins By insider.si.edu Published On :: Mon, 29 Mar 2010 14:31:29 +0000 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. Full Article Anthropology Research News Science & Nature evolution exhibitions extinction National Museum of Natural History
ir Japanese giant salamanders given to the National Zoo by Asa Zoological Park in Hiroshima By insider.si.edu Published On :: Fri, 23 Jul 2010 16:48:31 +0000 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. The post Japanese giant salamanders given to the National Zoo by Asa Zoological Park in Hiroshima appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature amphibian conservation endangered species new acquisitions Smithsonian's National Zoo veterinary medicine
ir New Zealand Embassy donates kiwi pair to National Zoo Breeding Science Center By insider.si.edu Published On :: Mon, 26 Jul 2010 17:53:48 +0000 Kiwis come to National Zoo. The Smithsonian’s National Zoo will be using a new kiwi pair donated by the New Zealand Embassy to establish a breeding science center. […] The post New Zealand Embassy donates kiwi pair to National Zoo Breeding Science Center appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature Spotlight birds
ir Scientists establish first frozen repository of Hawaiian coral By insider.si.edu Published On :: Wed, 18 Aug 2010 08:26:38 +0000 Unless action is taken now, coral reefs and many of the animals that depend on them may cease to exist within the next 40 years, causing the first global extinction of a worldwide ecosystem during current history. The post Scientists establish first frozen repository of Hawaiian coral appeared first on Smithsonian Insider. Full Article Marine Science Research News Science & Nature climate change conservation coral reefs endangered species extinction fungi greenhouse gas Smithsonian's National Zoo
ir Rapid Response telescope system spots first potentially hazardous asteroid By insider.si.edu Published On :: Tue, 28 Sep 2010 11:50:53 +0000 The Panoramic Survey Telescope & Rapid Response System (Pan-STARRS) PS1 telescope has discovered an asteroid about 150 feet in diameter that will come within 4 million miles of Earth in mid-October. The post Rapid Response telescope system spots first potentially hazardous asteroid appeared first on Smithsonian Insider. Full Article Research News Science & Nature asteroids astronomy astrophysics Center for Astrophysics | Harvard & Smithsonian rocks & minerals supernova
ir Genetic surprise: Magnificent frigatebird living on Galapagos Islands is distinct species By insider.si.edu Published On :: Tue, 28 Sep 2010 16:09:32 +0000 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. Full Article Animals Marine Science Research News Science & Nature birds Caribbean endangered species Migratory Bird Center National Museum of Natural History
ir For safety’s sake, Zoo’s lion cubs take first swim By insider.si.edu Published On :: Fri, 29 Oct 2010 12:00:18 +0000 For safety’s sake, the four eight-week-old cubs born to National Zoo lioness Shera were given a swim test on Oct. 26 in the moat of […] The post For safety’s sake, Zoo’s lion cubs take first swim appeared first on Smithsonian Insider. Full Article Animals Science & Nature Spotlight mammals Smithsonian's National Zoo veterinary medicine
ir One hundred sixty years after his birth a racehorse’s bones return to Lexington By insider.si.edu Published On :: Wed, 17 Nov 2010 13:51:00 +0000 Known as one of the greatest racehorses of his day and sire to more winning horses than any other American thoroughbred before or since, this Smithsonian loan returned the legendary Lexington's remains to the town of his birthplace some 160 years after he was born. The post One hundred sixty years after his birth a racehorse’s bones return to Lexington appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature conservation mammals National Museum of Natural History osteology
ir National Zoo and partners first to breed critically endangered tree frog By insider.si.edu Published On :: Thu, 18 Nov 2010 18:23:34 +0000 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. Full Article Animals Research News Science & Nature amphibian animal births biodiversity chytrid fungus conservation conservation biology endangered species extinction frogs Smithsonian's National Zoo veterinary medicine
ir Exurban development is changing communities of birds in Eastern Forests By insider.si.edu Published On :: Wed, 22 Dec 2010 12:33:43 +0000 Despite the general perception of exurban development as environmentally preferable to urban sprawl, this is not necessarily correct. Housing development is detrimental for natural bird communities even at low housing levels. The post Exurban development is changing communities of birds in Eastern Forests appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature biodiversity birds conservation conservation biology Migratory Bird Center Smithsonian's National Zoo
ir Environmental Research Center to help with Chesapeake Bay seagrass restoration By insider.si.edu Published On :: Wed, 22 Dec 2010 15:33:41 +0000 A research team from The Smithsonian Environmental Research Center and Virginia's Old Dominion University will be awarded $110,999 to develop a tool to help seagrass restorers predict which places will be the best for planting seagrasses, the Virginia Sea Grant has announced. The post Environmental Research Center to help with Chesapeake Bay seagrass restoration appeared first on Smithsonian Insider. Full Article Animals Marine Science Research News Science & Nature biodiversity Chesapeake Bay climate change conservation biology Smithsonian Environmental Research Center