Archives, Room Use Only - E608.K47 1890

Archives, Room Use Only - TK5745.S45 1864

Archives, Room Use Only - QC761.W54 1876

The Giants claimed Cooper Rush off waivers from their division rivals earlier this week. It makes sense given Rush's familiarity with new offensive coordinator Jason Garrett's offense. Rush can help teach it to starter Daniel Jones. Of course, the Giants don't expect Rush to play. Thus, they renegotiated Rush's deal, which was due to pay [more]

Lockdown effect: Retailers eye renegotiating contracts at malls

State records 31 new COVID-19 cases

This review discusses the state of the field of single-crystal diffuse scattering (SCDS), including detectors, data collection and the modelling techniques. High quality, three-dimensional volumes of SCDS data can now be collected at synchrotron light sources, allowing increasingly detailed and quantitative analyses to be undertaken.

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Reductive cyclization of 1,3,5-triphenyl- and 3-(2-meth­oxy­phen­yl)-1,5-di­phenyl­pentane-1,5-diones by zinc in acetic acid medium leads to the formation of 1,2,4-tri­phenyl­cyclo­pentane-1,2-diol [1,2,4-Ph3C5H5-1,2-(OH)2, C23H22O2, (I)] and 4-(2-meth­oxy­phen­yl)-1,2-di­phenyl­cyclo­pentane-1,2-diol [4-(2-MeOC6H4)-1,2-Ph2C5H5-1,2-(OH)2, C24H24O3, (II)]. Their single crystals have been obtained by crystallization from a THF/hexane solvent mixture. Diols (I) and (II) crystallize in ortho­rhom­bic (Pbca) and triclinic (Poverline{1}) space groups, respectively, at 150 K. Their asymmetric units comprise one [in the case of (I)] and three [in the case of (II)] crystallographically independent mol­ecules of the achiral (1R,2S,4r)-diol isomer. Each hydroxyl group is involved in one intra­molecular and one inter­molecular O—H⋯O hydrogen bond, forming one-dimensional chains. Compounds (I) and (II) have been used successfully as precatalyst activators for the ring-opening polymerization of ∊-caprolactone.

In the past three years, Dirac half-metals (DHMs) have attracted considerable attention and become a high-profile topic in spintronics becuase of their excellent physical properties such as 100% spin polarization and massless Dirac fermions. Two-dimensional DHMs proposed recently have not yet been experimentally synthesized and thus remain theoretical. As a result, their characteristics cannot be experimentally confirmed. In addition, many theoretically predicted Dirac materials have only a single cone, resulting in a nonlinear electromagnetic response with insufficient intensity and inadequate transport carrier efficiency near the Fermi level. Therefore, after several attempts, we have focused on a novel class of DHMs with multiple Dirac crossings to address the above limitations. In particular, we direct our attention to three-dimensional bulk materials. In this study, the discovery via first principles of an experimentally synthesized DHM LaNiO3 with many Dirac cones and complete spin polarization near the Fermi level is reported. It is also shown that the crystal structures of these materials are strongly correlated with their physical properties. The results indicate that many rhombohedral materials with the general formula LnNiO3 (Ln = La, Ce, Nd, Pm, Gd, Tb, Dy, Ho, Er, Lu) in the space group R3c are potential DHMs with multiple Dirac cones.

Here, an analysis is performed of how uncorrected antisymmetric aberrations, such as coma and trefoil, affect cryo-EM single-particle reconstruction (SPR) results, and an analytical formula quantifying information loss owing to their presence is inferred that explains why Fourier-shell coefficient-based statistics may report significantly overestimated resolution if these aberrations are not fully corrected. The analysis is validated with reference-based aberration refinement for two cryo-EM SPR data sets acquired with a 200 kV microscope in the presence of coma exceeding 40 µm, and 2.3 and 2.7 Å reconstructions for 144 and 173 kDa particles, respectively, were obtained. The results provide a description of an efficient approach for assessing information loss in cryo-EM SPR data acquired in the presence of higher order aberrations, and address inconsistent guidelines regarding the level of aberrations that is acceptable in cryo-EM SPR experiments.

Two commonly encountered bottlenecks in the structure determination of a protein by X-ray crystallography are screening for conditions that give high-quality crystals and, in the case of novel structures, finding derivatization conditions for experimental phasing. In this study, the phasing molecule 5-amino-2,4,6-triiodoisophthalic acid (I3C) was added to a random microseed matrix screen to generate high-quality crystals derivatized with I3C in a single optimization experiment. I3C, often referred to as the magic triangle, contains an aromatic ring scaffold with three bound I atoms. This approach was applied to efficiently phase the structures of hen egg-white lysozyme and the N-terminal domain of the Orf11 protein from Staphylococcus phage P68 (Orf11 NTD) using SAD phasing. The structure of Orf11 NTD suggests that it may play a role as a virion-associated lysin or endolysin.

Human carbonic anhydrase IX (CA IX) expression is upregulated in hypoxic solid tumours, promoting cell survival and metastasis. This observation has made CA IX a target for the development of CA isoform-selective inhibitors. To enable structural studies of CA IX–inhibitor complexes using X-ray and neutron crystallography, a CA IX surface variant (CA IXSV; the catalytic domain with six surface amino-acid substitutions) has been developed that can be routinely crystallized. Here, the preparation of protiated (H/H), H/D-exchanged (H/D) and deuterated (D/D) CA IXSV for crystallographic studies and their structural comparison are described. Four CA IXSV X-ray crystal structures are compared: two H/H crystal forms, an H/D crystal form and a D/D crystal form. The overall active-site organization in each version is essentially the same, with only minor positional changes in active-site solvent, which may be owing to deuteration and/or resolution differences. Analysis of the crystal unit-cell packing reveals different crystallographic and noncrystallographic dimers of CA IXSV compared with previous reports. To our knowledge, this is the first report comparing three different deuterium-labelled crystal structures of the same protein, marking an important step in validating the active-site structure of CA IXSV for neutron protein crystallography.

Although often presented as taking single `snapshots' of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes residual electron and anomalous density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data-collection and analysis strategy for partially occupied iodine anomalous signals. Using the long-wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as ∼12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that re-measured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2–3 × 10−4 (ΔE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ΔE/E = 3 × 10−3) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.

The phase transition of E-vanillyl oxime {1-[(E)-(hydroxyimino)methyl]-4-hydroxy-3-methoxybenzene, C8H9NO3} has been analysed by single-crystal and powder X-ray diffraction. The high-temperature (HT) phase (P21/a, Z' = 1) transforms into the low-temperature (LT) phase (threefold superstructure, Poverline{1}, Z' = 6) at ca 190 K. The point operations lost on cooling, {m[010], 2[010]}, are retained as twin operations and constitute the twin law. The screw rotations and glide reflections are retained in the LT phase as partial operations acting on a subset of Euclidean space {b E}^3. The full symmetry of the LT phase, including partial operations, is described by a disconnected space groupoid which is built of three connected components.

The optical design of a Hettrick–Underwood-style soft X-ray spectrometer with Wolter type 1 mirrors is presented. The spectrometer with a nominal length of 3.1 m can achieve a high resolving power (resolving power higher than 10000) in the soft X-ray regime when a small source beam (<3 µm in the grating dispersion direction) and small pixel detector (5 µm effective pixel size) are used. Adding Wolter mirrors to the spectrometer before its dispersive elements can realize the spatial imaging capability, which finds applications in the spectroscopic studies of spatially dependent electronic structures in tandem catalysts, heterostructures, etc. In the pump–probe experiments where the pump beam perturbs the materials followed by the time-delayed probe beam to reveal the transient evolution of electronic structures, the imaging capability of the Wolter mirrors can offer the pixel-equivalent femtosecond time delay between the pump and probe beams when their wavefronts are not collinear. In combination with some special sample handing systems, such as liquid jets and droplets, the imaging capability can also be used to study the time-dependent electronic structure of chemical transformation spanning multiple time domains from microseconds to nanoseconds. The proposed Wolter mirrors can also be adopted to the existing soft X-ray spectrometers that use the Hettrick–Underwood optical scheme, expanding their capabilities in materials research.

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.

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.