Dose, exposure time, and resolution in Serial X-ray Crystallography

The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available molecular and X-ray fluxes and molecular alignment. Orientation of the diffracting molecules is achieved by laser alignment. We evaluate the incident X-ray fluence (energy/area) required to obtain a given resolution from (1) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (2) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency cut off of the transfer function following iterative solution of the phase problem, and reconstruction of an electron density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate counting time and the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. We confirm an inverse fourth power dependence of exposure time on resolution, with important implications for all coherent X-ray imaging. We find that multiple single-file protein beams will be needed for sub-nanometer resolution on current third generation synchrotrons, but not on fourth generation designs, where reconstruction of secondary protein structure at a resolution of 0.7 nm should be possible with short exposures.Comment: 19 pages, 7 figures, 1 tabl

One-Center Charge Transfer Transitions in Manganites

In frames of a rather conventional cluster approach, which combines the crystal field and the ligand field models we have considered different charge transfer (CT) states and O 2p-Mn 3d CT transitions in MnO$_{6}^{9-}$ octahedra. The many-electron dipole transition matrix elements were calculated using the Racah algebra for the cubic point group. Simple "local" approximation allowed to calculate the relative intensity for all dipole-allowed $\pi -\pi$ and $\sigma -\sigma$ CT transitions. We present a self-consistent description of the CT bands in insulating stoichiometric LaMn$^{3+}$O$_3$ compound with the only Mn$^{3+}$ valent state and idealized octahedral MnO$_{6}^{9-}$ centers which allows to substantially correct the current interpretation of the optical spectra. Our analysis shows the multi-band structure of the CT optical response with the weak low-energy edge at 1.7 eV, associated with forbidden $t_{1g}(\pi)-e_{g}$ transition and a series of the weak and strong dipole-allowed high-energy transitions starting from 2.5 and 4.5 eV, respectively, and extending up to nearly 11 eV. The most intensive features are associated with two strong composite bands near $4.6\div 4.7$ eV and $8\div 9$ eV, respectively, resulting from the superposition of the dipole-allowed $\sigma -\sigma$ and $\pi -\pi$ CT transitions. These predictions are in good agreement with experimental spectra. The experimental data point to a strong overscreening of the crystal field parameter $Dq$ in the CT states of MnO$_{6}^{9-}$ centers.Comment: 10 pages, 3 figure

Electronic structure investigation of CoO by means of soft X-ray scattering

The electronic structure of CoO is studied by resonant inelastic soft X-ray scattering spectroscopy using photon energies across the Co 2p absorption edges. The different spectral contributions from the energy-loss structures are identified as Raman scattering due to d-d and charge-transfer excitations. For excitation energies close to the L3 resonance, the spectral features are dominated by quartet-quartet and quartet-doublet transitions of the 3d7 configuration. At excitation energies corresponding to the satellites in the Co 2p X-ray absorption spectrum of CoO, the emission features are instead dominated by charge-transfer transitions to the 3d8L-1 final state. The spectra are interpreted and discussed with the support of simulations within the single impurity Anderson model with full multiplet effects which are found to yield consistent spectral functions to the experimental data.Comment: 8 pages, 2 figures, 2 tables, http://link.aps.org/doi/10.1103/PhysRevB.65.20510

Monitoring carbon dioxide concentration for early detection of spoilage in stored grain

Field experiments were conducted in storage silos to evaluate carbon dioxide sensors to monitor spoilage in grain prior to spoilage detection by traditional methods such as visual inspections and temperature cables. Carbon dioxide concentrations in the storage silo were monitored up to eight months and correlated to the presence of stored-product insects, molds and mycotoxin levels in the stored grain. The data showed that safe grain storage was observed at CO2 concentrations of 400 to 500 ppm. Higher concentrations of CO2 clearly showed mold spoilage or insect activity inside the grain storage silo. Carbon dioxide concentrations of 500 to 1200 ppm indicated onset of mold infection where as CO2 concentrations of 1500 to 4000 ppm and beyond clearly indicated severe mold infection or stored-product insects infestation. The percent kernel infection was in the range of 30% for CO2 concentrations of 500 to 1000 ppm to 90% for CO2 concentrations of 9000 ppm. Fungal concentrations were in the range of 2.0 ×102 colony forming units per gram (cfu/g) at 500 ppm CO2 concentration to 6.5 ×107 cfu/g at 9000 ppm CO2 concentration. Fungi of genera Aspergillus spp., Penicillium spp., and Fusarium spp. were isolated from spoiled grain. High concentration of fungi and presence of mycotoxins (aflatoxin: 2 ppb and Deoxynivalenol (DON): 1 ppm) were correlated with high CO2 concentration in the silos. The findings from this research will be helpful in providing more timely information regarding safe storage limits, aeration requirements and costs of spoilage mitigation measures such as turning, aerating and fumigating grain. Additionally, it will provide information on preventive stored grain quality management practices that should reduce residue levels of mycotoxins, pesticides and other foreign material in our food supply. The CO2 monitoring technology will increase the quality and quantity of stored grain, while saving the U.S. and global grain production, handling and processing industry millions of dollars annually. Keywords: Carbon dioxide, Grain storage, Stored-product insects, Mold and mycotoxi

Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility

Escherichia coli endonuclease VIII (Nei) excises oxidized pyrimidines from DNA. It shares significant sequence homology and similar mechanism with Fpg, a bacterial 8-oxoguanine glycosylase. The structure of a covalent Nei–DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. Several Fpg structures have also been reported; however, analysis of structural dynamics of Fpg/Nei family proteins has been hindered by the lack of structures of uncomplexed and DNA-bound enzymes from the same source. We report a 2.8 Å resolution structure of free wild-type Nei and two structures of its inactive mutants, Nei-E2A (2.3 Å) and Nei-R252A (2.05 Å). All three structures are virtually identical, demonstrating that the mutations did not affect the overall conformation of the protein in its free state. The structures show a significant conformational change compared with the Nei structure in its complex with DNA, reflecting a ∼50° rotation of the two main domains of the enzyme. Such interdomain flexibility has not been reported previously for any DNA glycosylase and may present the first evidence for a global DNA-induced conformational change in this class of enzymes. Several local but functionally relevant structural changes are also evident in other parts of the enzyme

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach

Decoupling property of the supersymmetric Higgs sector with four doublets

In supersymmetric standard models with multi Higgs doublet fields, selfcoupling constants in the Higgs potential come only from the D-terms at the tree level. We investigate the decoupling property of additional two heavier Higgs doublet fields in the supersymmetric standard model with four Higgs doublets. In particular, we study how they can modify the predictions on the quantities well predicted in the minimal supersymmetric standard model (MSSM), when the extra doublet fields are rather heavy to be measured at collider experiments. The B-term mixing between these extra heavy Higgs bosons and the relatively light MSSM-like Higgs bosons can significantly change the predictions in the MSSM such as on the masses of MSSM-like Higgs bosons as well as the mixing angle for the two light CP-even scalar states. We first give formulae for deviations in the observables of the MSSM in the decoupling region for the extra two doublet fields. We then examine possible deviations in the Higgs sector numerically, and discuss their phenomenological implications.Comment: 26 pages, 24 figures, text sligtly modified,version to appear in Journal of High Energy Physic