Showing papers in "Journal of Synchrotron Radiation in 2005"
TL;DR: A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented, based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit.
Abstract: A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.
12,505 citations
TL;DR: A new facility for high-pressure diffraction and spectroscopy using diamond anvil high- pressure cells has been built at the Advanced Light Source and the experimental enclosure contains an automated beam-positioning system, a set of slits, ion chambers, the sample positioning goniometry and area detector.
Abstract: A new facility for high-pressure diffraction and spectroscopy using diamond anvil high-pressure cells has been built at the Advanced Light Source on Beamline 12.2.2. This beamline benefits from the hard X-radiation generated by a 6 Tesla superconducting bending magnet (superbend). Useful x-ray flux is available between 5 keV and 35 keV. The radiation is transferred from the superbend to the experimental enclosure by the brightness preserving optics of the beamline. These optics are comprised of: a plane parabola collimating mirror (M1), followed by a Kohzu monochromator vessel with a Si(111) crystals (E/{Delta}E {approx} 7000) and a W/B{sub 4}C multilayer (E/{Delta}E {approx} 100), and then a toroidal focusing mirror (M2) with variable focusing distance. The experimental enclosure contains an automated beam positioning system, a set of slits, ion chambers, the sample positioning goniometry and area detectors (CCD or image-plate detector). Future developments aim at the installation of a second end station dedicated for in situ laser-heating on one hand and a dedicated high-pressure single-crystal station, applying both monochromatic as well as polychromatic techniques.
140 citations
TL;DR: Calculations indicate that significant reductions in radiation damage could occur for crystals of a few microm in size, and the benefits would be greater when operating at higher energies.
Abstract: The primary event which occurs when an X-ray photon of energy less than 30 keV is absorbed in a protein crystal (or other organic material) is the production of a photoelectron with a similar energy to that of the absorbed photon. The electron then scatters inelastically off the surrounding material losing energy in the process. This reduction in energy takes place over track lengths of a few µm for 20 keV electrons. The vector distances between the initial and final positions of the photoelectrons are less than the track lengths owing to the non-linear tracks followed by the electrons. For crystals with smaller dimensions than the vector distances, a significant proportion of the energy could leave the crystal with the high-energy electrons. This could provide an advantage in terms of reduced radiation damage. In order to estimate the possible benefits, calculations of the electron tracks are given, initially using the continuous slowing-down approximation. A Monte Carlo approach is then used to provide more accurate values of the vector distance travelled by electrons inside a protein crystal. The calculations indicate that significant reductions in radiation damage could occur for crystals of a few µm in size. The benefits would be greater when operating at higher energies. In addition, a scheme for realising the possible benefits in a practical situation is described. This could then form the basis of trial experiments.
137 citations
TL;DR: A new state-of-the art synchrotron beamline fully optimized for monochromatic X-ray diffraction at high pressure and high (or low) temperature is presented and exhibits outstanding performance in terms of photon flux and focusing capabilities.
Abstract: A new state-of-the art synchrotron beamline fully optimized for monochromatic X-ray diffraction at high pressure and high (or low) temperature is presented. In comparison with the old high-pressure beamline ID30, this new beamline exhibits outstanding performance in terms of photon flux and focusing capabilities. The main components of this new instrument will be described in detail and compared with the performance of beamline ID30. In particular, the choices in terms of X-ray source, X-ray optics, sample environment and detectors are discussed. The first results of the beamline commissioning are presented.
128 citations
TL;DR: Although progress is being made, the understanding of radiation damage is far from complete and methods for recognizing the damage and treating the data are being made available but they are still at an early stage of development.
Abstract: Interest in radiation damage is growing rapidly owing to the surge in macromolecular crystallography experiments carried out at modern brilliant synchrotron macromolecular crystallography beamlines. Work on the characterization of radiation damage in cryocooled protein crystals is starting to have some impact on our understanding of the problem and of how damage might be affecting both the process of structure solution and the actual structure obtained. A brief review of the most recent developments is given together with an assessment of the remaining problems. Although progress is being made, the understanding of radiation damage is far from complete. Methods for recognizing the damage and treating the data are being made available but they are still at an early stage of development.
124 citations
TL;DR: A Rietveld method is described which extracts information on crystal structure, texture and microstructure directly from two-dimensional synchrotron diffraction images, advantageous over conventional texture analysis that relies on individual diffraction peaks, particularly for low-symmetry materials with many overlapping peaks and images with a poor peak-to-background ratio.
Abstract: A Rietveld method is described which extracts information on crystal structure, texture and microstructure directly from two-dimensional synchrotron diffraction images. This is advantageous over conventional texture analysis that relies on individual diffraction peaks, particularly for low-symmetry materials with many overlapping peaks and images with a poor peak-to-background ratio. The method is applied to two mineralized biological samples with hydroxylapatite fabrics: an ossified pachycephalosaurid dinosaur tendon and an Atlantic salmon scale. Both are measured using monochromatic synchrotron X-rays. The dinosaur tendon has very strongly oriented crystals with c-axes parallel to the tendon direction. The salmon scale displays a weak texture.
116 citations
TL;DR: Comparison of conventional normalization methods with MBACK demonstrates that the new normalization method is not sensitive to the shape of the background function, thus allowing accurate comparison of data collected in transmission mode with data collected using fluorescence ion chambers or solid-state fluorescence detectors.
Abstract: Accurate normalization of X-ray absorption data is essential for quantitative analysis of near-edge features. A method, implemented as the program MBACK, to normalize X-ray absorption data to tabulated mass absorption coefficients is described. Comparison of conventional normalization methods with MBACK demonstrates that the new normalization method is not sensitive to the shape of the background function, thus allowing accurate comparison of data collected in transmission mode with data collected using fluorescence ion chambers or solid-state fluorescence detectors. The new method is shown to have better reliability and consistency and smaller errors than conventional normalization methods. The sensitivity of the new normalization method is illustrated by analysis of data collected during an equilibrium titration.
88 citations
TL;DR: A dispersion-compensation method to remove the cube-size effect from the resolution function of diced analyzer crystals using a position-sensitive two-dimensional pixel detector is presented, allowing a substantial increase in the resolving power without any loss of signal intensity.
Abstract: A dispersion-compensation method to remove the cube-size effect from the resolution function of diced analyzer crystals using a position-sensitive two-dimensional pixel detector is presented. For demonstration, a resolution of 23 meV was achieved with a spectrometer based on a 1 m Rowland circle and a diced Si(555) analyzer crystal in a near-backscattering geometry, with a Bragg angle of 88.5°. In this geometry the spectrometer equipped with a traditional position-insensitive detector provides a resolution of 190 meV. The dispersion-compensation method thus allows a substantial increase in the resolving power without any loss of signal intensity.
84 citations
TL;DR: The Troika II beamline at the European Synchrotron Radiation Facility was conceived as a versatile beamline for the study of liquid and solid interfaces, combining grazing-incidence diffraction, X-ray reflectivity and grazing- incidence small-angle scattering in a single instrument.
Abstract: The Troika II beamline at the European Synchrotron Radiation Facility was conceived as a versatile beamline for the study of liquid and solid interfaces, combining grazing-incidence diffraction, X-ray reflectivity and grazing-incidence small-angle scattering in a single instrument. Scattering experiments can be performed both in horizontal and in vertical scattering geometry. Additional options are the use of analyzer crystals for high-resolution studies in both the horizontal and the vertical scattering geometry as well as the use of a horizontal microfocusing mirror for experiments requiring very high flux onto the sample. Here, the way in which the features of the beamline have been exploited in selected recent experiments is described.
80 citations
TL;DR: The theory, instrumentation and application of polychromatic microdiffraction are described and three-dimensional distributions of crystalline morphology including grain boundaries, triple points, second phases and inclusions can all be mapped.
Abstract: Polychromatic X-ray microdiffraction is an emerging tool for studying mesoscale structure and dynamics Crystalline phase, orientation (texture), elastic and plastic strain can be nondestructively mapped in three dimensions with good spatial and angular resolution Local crystallographic orientation can be determined to ∼001° and elastic strain tensor elements can be measured with a resolution of ∼10−4 or better Complete strain tensor information can be obtained by augmenting polychromatic microdiffraction with a monochromatic measurement of one Laue-reflection energy With differential-aperture depth profiling, volumes tens to hundreds of micrometers below the surface are accessible so that three-dimensional distributions of crystalline morphology including grain boundaries, triple points, second phases and inclusions can all be mapped Volume elements below 025 µm3 are routinely resolved so that the grain boundary structure of most materials can be characterized Here the theory, instrumentation and application of polychromatic microdiffraction are described
78 citations
TL;DR: The results of RADDOSE can and will in the future be used to inform the data collection procedure as it sets a theoretical upper limit on the total exposure time at a certain X-ray source.
Abstract: The lifetime of a macromolecular crystal in an X-ray beam is assumed to be limited by the absorbed dose. This dose, expressed in Gray (Gy = J kg−1), is a function of a number of parameters: the absorption coefficients of the constituent atoms of the crystal, the number of molecules per asymmetric unit, the beam energy, flux, size and profile, the crystal size, and the total irradiation time. The effects of these variables on the predicted absorbed dose, calculated using the program RADDOSE, are discussed and are illustrated with reference to the irradiation of a selenomethionine protein crystal of unknown structure. The results of RADDOSE can and will in the future be used to inform the data collection procedure as it sets a theoretical upper limit on the total exposure time at a certain X-ray source. However, as illustrated with an example for which the experimental data are compared with prediction, the actual lifetime of a crystal could become shorter in those cases where specific damage breaks down crucial crystal contacts.
TL;DR: The combination of X-ray microdiffraction and microfluidics is used to investigate the dynamic behaviour of soft materials to improve structural characterization and the influence of strain applied to these materials can be tested.
Abstract: The combination of X-ray microdiffraction and microfluidics is used to investigate the dynamic behaviour of soft materials. A microfocused X-ray beam enables the observation of the influence of droplet formation on the nanostructure of a smectic liquid crystal in water. Using a hydrodynamic focusing device, the evolution of the intercalation of DNA into multilamellar membranes can be studied. Owing to the elongational flow at the centre of this device, alignment of the material is induced which allows for an improved structural characterization. Furthermore, the influence of strain applied to these materials can be tested.
TL;DR: Beamline Scheduling Software (BSS) has been developed for the schedule management and equipment control of the RIKEN Structural Genomics Beamlines I and II.
Abstract: Beamline Scheduling Software (BSS) has been developed for the schedule management and equipment control of the RIKEN Structural Genomics Beamlines I and II (BL26B1 and BL26B2 at SPring-8). The beamline operation is automated with a sample-changer robot and a database system. The experimental schedule is registered to BSS as a list of diffraction measurements for numbers of protein crystals. BSS implements the beamline operation communicating with beamline instruments through the computer network. The RIKEN Structural Genomics Beamline I (BL26B1) opened for users using BSS in October 2002, and the automatic operation was implemented at BL26B2 in October 2003.
TL;DR: ExAFS spectra of organohalogen compounds (both iodine and bromine) can be used to discriminate between aliphatic and aromatic compounds and there are differences both in the distances from the halogens to the first shell of C atoms, which are shorter for aromatic compounds, and in the patterns of shells in the Fourier transforms.
Abstract: X-ray absorption spectra of a number of organic iodine and bromine compounds of biological relevance, as well as of a series of iodine compounds with different oxidation states, have been measured. The iodine K-edge spectra (XANES) are found to be relatively featureless but the position of the edge is found to be sensitive to formal valence (among other factors), and the edge shape to the number of bound O atoms. EXAFS spectra of organohalogen compounds (both iodine and bromine) can be used to discriminate between aliphatic and aromatic compounds. There are differences both in the distances from the halogens to the first shell of C atoms, which are shorter for aromatic compounds, and in the patterns of shells in the Fourier transforms. This result is expected to be relevant to studies at these edges in biological systems.
TL;DR: Highly oriented native cellulose fibres (flax) and softwood (pine) have been investigated by means of X-ray diffraction, revealing a change of orientation of cellulose microfibrils in materials with tensile strain.
Abstract: Highly oriented native cellulose fibres (flax) and softwood (pine) have been investigated by means of X-ray diffraction. Local structural information was obtained by using X-ray microbeams. Tensile tests were performed in situ, revealing a change of orientation of cellulose microfibrils in materials with tensile strain. In flax fibres, the microfibrils rotate during the first percent of stretching, into a more parallel orientation with respect to the fibre axis. For wood, a decrease of orientation with the onset of strain hardening is found for the first time.
TL;DR: A new high-speed high-repetition-rate X-ray beam shutter for time-resolved photocrystallography at synchrotron sources has been developed and tested and provides high accuracy and efficient use of X-rays at a modest cost.
Abstract: A new high-speed high-repetition-rate X-ray beam shutter for time-resolved photocrystallography at synchrotron sources has been developed and tested. The new design is based on a commercially existing DC servomotor and a frequency-lock control capable linear amplifier. Accurate speed control combined with an air bearing results in extremely low jitter in the motor rotation. Measured jitter at rotation speeds of 12000 to 30000 r min-1 is less than 2 ns at a 6sigma confidence level. The chopper disc is interchangeable, allowing maximum flexibility. The chopper disc currently installed has 45 radial slots which allows synchronization from the 12th to the 20th subfrequencies of the orbit frequency of the Advanced Photon Source storage ring, corresponding to X-ray pulse frequencies of 13.6 to 22.6 kHz. At 30000 r min-1 the opening time window with a 350 microm slot size is 2.11 micros, and correspondingly less with smaller openings, which may be compared with the 3.68 micros orbit time of the Advanced Photon Source. The shutter provides high accuracy and efficient use of X-rays at a modest cost.
TL;DR: The crystal structure of hexagonal L-cystine has been determined at room temperature at pressures between 0.4 and 3.7 GPa; unit-cell dimensions were measured up to 6.4 GPa.
Abstract: The crystal structure of hexagonal l-cystine has been determined at room temperature at pressures between 0.4 and 3.7 GPa; unit-cell dimensions were measured up to 6.4 GPa. The structure of this phase consists of molecules in their zwitterionic form, and crystallizes in the hexagonal space group P6122. The structure consists of hydrogen-bonded layers which are strongly reminiscent of those seen in α-glycine, and consist of R_4^4(16) hydrogen-bonded ring motifs. These layers are connected on one side by the disulfide bridges within the cystine molecules, and on the other by NH⋯O hydrogen bonds to other glycine-like layers. The most compressible unit-cell dimension, and the direction of greatest strain in the structure, is along the c-axis, and application of pressure pushes the layers closer together. The compression occurs approximately equally in the regions of the interlayer hydrogen bonds and the disulfide bridges; in the latter, changes in the C—S—S—C torsion angles allow the cystine molecules to act like springs. The effects of pressure can be interpreted in terms of closing-up of voids in the structure, and this leads to (i) a lessening of the N—C—C—O and C—S—S—C torsional angles, (ii) shortening of the N—H⋯O hydrogen bonds by 0.10–0.60 A and (iii) a further shortening of an already short S⋯S contact from 3.444 (4) A to 3.264 (4) A.
TL;DR: The utilization and the potential of softer and soft X-rays in macromolecular crystallography as well as the challenges associated with the corresponding diffraction experiments and their possible remedies are reviewed.
Abstract: The utilization and the potential of softer and soft X-rays in macromolecular crystallography as well as the challenges associated with the corresponding diffraction experiments and their possible remedies are reviewed.
TL;DR: This pioneering experiment indicates that this hybrid imaging technique might permit simultaneous advantage of the specific features of the two imaging methods to be taken.
Abstract: The combination of X-ray 'propagation-based' and 'analyzer-based' phase-contrast imaging with a perfect crystal-analyzer is investigated. The image pattern produced using this 'hybrid' imaging technique presents peculiar features that can be interpreted as a mixture of the two independent phase-contrast signals. A quantitative analysis has been performed in terms of signal-to-noise ratio for the three techniques considered in this paper. Results show that in the 'hybrid imaging' technique this parameter has a weaker dependence on the angular alignment of the crystal analyser with respect to the 'analyser-based' imaging. This pioneering experiment indicates that this hybrid imaging technique might permit simultaneous advantage of the specific features of the two imaging methods to be taken.
TL;DR: High-pressure powder and single-crystal diffraction, spectroscopy, inelastic scattering, radiography, and infrared spectrum analysis have been studied in this article, and the results have implications for a variety of problems in physics, chemistry, materials science, geoscience, planetary science and biology.
Abstract: With the steady development of static high-pressure techniques in recent years, it is now possible to probe in increasing detail the novel behavior of materials subjected to extreme conditions of multimegabar pressures (>300 GPa) and temperatures from cryogenic states to thousands of degrees. By and large, the growth in this area has been made possible by accelerating developments in diamond-anvil cell methods coupled with new synchrotron radiation techniques. Significant advances have occurred in high-pressure powder and single-crystal diffraction, spectroscopy, inelastic scattering, radiography, and infrared spectroscopy. A brief overview of selected highlights in each of these classes of experiments is presented that illustrate both the state-of-the-art as well as current technical and scientific challenges. The experiments have been made possible by the development of a spectrum of new techniques at both third- and second-generation high-energy sources together with key advances in high-pressure technology. The results have implications for a variety of problems in physics, chemistry, materials science, geoscience, planetary science, and biology.
TL;DR: A review of the recent developments of the ID22 beamline and a detailed description of its capabilities through examples from different fields of applications is presented.
Abstract: The ID22 beamline is dedicated to hard X-ray microanalysis allowing the combination of fluorescence, spectroscopy, diffraction and tomography techniques in a wide energy range from 6 to 70 keV. The recent installation of an in-vacuum undulator, a new sample stage and the adaptation of various focusing optics has contributed to a great improvement in the capabilities of the beamline, which is now accessed by a wide user community issued from medical, earth and environmental science, archaeology and material science. Many applications requiring low detection limits for localization/speciation of trace elements together with structural analysis have been developed at the beamline on the (sub)micrometer scale. The possibility of combining simultaneously different analytical probes offers the opportunity of a thorough study of a given sample or scientific problem. This paper presents a review of the recent developments of the beamline and a detailed description of its capabilities through examples from different fields of applications.
TL;DR: An overview of facilities for high-pressure research with the diamond anvil cell (DAC) at the GeoSoilEnviroCARS (GSECARS) sector at the Advanced Photon Source is presented.
Abstract: An overview of facilities for high-pressure research with the diamond anvil cell (DAC) at the GeoSoilEnviroCARS (GSECARS) sector at the Advanced Photon Source (Argonne, Illinois) is presented. There are three operational experimental stations (13-ID-C, 13-ID-D and 13-BM-D) where DAC instrumentation is installed for various types of experiments at high pressure and extreme temperature conditions. A fourth station (13-BM-C) is under construction and will be operational in 2006. While most X-ray diffraction experiments have been undertaken with powder samples so far, there is a growing demand for single-crystal diffraction (SCD) at high pressure. As one of the principal components at GSECARS, SCD is currently under rapid development. Other relevant techniques have also been developed for obtaining complementary information from powder or single-crystal samples at high pressure. For example, an on-line Brillouin system is installed and operational at 13-BM-D for acoustic velocity and single-crystal elasticity determinations. In addition, various X-ray spectroscopy techniques (e.g. X-ray emission and X-ray Raman) are employed for measuring electronic and magnetic properties. Future developments are discussed with the DAC program at GSECARS.
TL;DR: In this article, the effect of radiation damage on macromolecular structure determination by single-wavelength anomalous dispersion (SAD) was quantified at the Se K-edge, where the exploitable signal can be less than a few percent.
Abstract: In the accurate estimation of small signals, redundancy of observations is often seen as an essential tool for the experimenter. This is particularly true during macromolecular structure determination by single-wavelength anomalous dispersion (SAD), where the exploitable signal can be less than a few percent. At the most intense undulator synchrotron beamlines, the effect of radiation damage can be such that all usable signal is obscured. Here the magnitude of this effect in experiments performed at the Se K-edge is quantified. Six successive data sets were collected on the same crystal, interspersed with two exposures to the X-ray beam during which data were not collected. It is shown that the very first data set has excellent phasing statistics, whereas these statistics degrade for the later data sets. Merging several data sets into one, highly redundant, data set only gave moderate improvements as a result of the presence of radiation damage. Part of the damage could be corrected for using a linear interpolation scheme. Interpolation of the data to a low-dose as well as to a high-dose data set allowed us to combine the SAD method with the radiation-damage induced phasing (RIP) technique, which further improved the experimental phases, especially after density modification. Some recommendations are given on how to mitigate the effect of radiation damage during structure determination.
TL;DR: Research at the Advanced Photon Source is described, illustrating the opportunities for ultrafast diffraction with some recent work on the generation of impulsive strain, coherent phonon generation and supersonic diffusion of electron-hole plasmas.
Abstract: Ultrafast X-ray experiments at synchrotron sources hold tremendous promise for measuring the atomistic dynamics of materials under a wide variety of transient conditions. In particular, the marriage of synchrotron radiation and ultrafast laser technology is opening up a new frontier of materials research. Structural changes initiated by femtosecond laser pulses can be tracked in real time using time-resolved X-ray diffraction on picosecond time scales or shorter. Here, research at the Advanced Photon Source is described, illustrating the opportunities for ultrafast diffraction with some recent work on the generation of impulsive strain, coherent phonon generation and supersonic diffusion of electron-hole plasmas. The flexibility of time-resolved Bragg and Laue diffraction geometries are both utilized to illuminate the strain generation and evolution process. Time-resolved X-ray science will become increasingly important with the construction of linac-based ultrafast X-ray sources.
TL;DR: This study demonstrates the use of monochromatic synchrotron X-ray radiation of 40 keV for high-precision equation-of-state studies on sets of single crystals analysed individually in the same diamond-anvil pressure cell.
Abstract: This study demonstrates the use of monochromatic synchrotron X-ray radiation of 40 keV for high-precision equation-of-state studies on sets of single crystals analysed individually in the same diamond-anvil pressure cell. Angle-dispersive zone-axis diffraction patterns were obtained from crystals of wustite-Fe0.93O and magnesiowustite-(Mg0.73Fe0.27)O to 51 GPa in a hydrostatic helium pressure medium. The rhombohedral phase of Fe0.93O was observed above 23 GPa, and its isothermal bulk modulus (K0) was determined to be 134 (±4) GPa, assuming K′ = 4. The rhombohedral phase of Fe0.93O is more compressible than B1-structured Fe0.93O, with K0 = 146 (±2) GPa. Magnesiowustite-(Mg0.73Fe0.27)O remains cubic over the experimental pressure range, and has a bulk modulus of 154 (±3) GPa with K′ = 4.0 (±0.1).
TL;DR: The collagen diffraction patterns of human aortas under uniaxial tensile test conditions have been investigated by synchrotron small-angle X-ray scattering and show a direct relation between the orientation and extension of the collagen fibers on the nanoscopic level and the macroscopic stress and strain.
Abstract: The collagen diffraction patterns of human aortas under uniaxial tensile test conditions have been investigated by synchrotron small-angle X-ray scattering. Using a recently designed tensile testing device the orientation and d-spacing of the collagen fibers in the adventitial layer have been measured in situ with the macroscopic force and sample stretching under physiological conditions. The results show a direct relation between the orientation and extension of the collagen fibers on the nanoscopic level and the macroscopic stress and strain. This is attributed first to a straightening, second to a reorientation of the collagen fibers, and third to an uptake of the increasing loads by the collagen fibers.
TL;DR: By perfecting each aspect of the fabrication, it is shown that spherically bent Si analyzers can provide the required energy resolution, and such analyzers have been successfully produced and have greatly improved the energy resolution in standard spheric bent analyzers.
Abstract: Resonant inelastic X-ray scattering with very high energy resolution is a promising technique for investigating the electronic structure of strongly correlated materials. The demands for this technique are analyzers which deliver an energy resolution of the order of 200 meV full width at half-maximum or below, at energies corresponding to the K-edges of transition metals (Cu, Ni, Co etc.). To date, high resolution under these conditions has been achieved only with diced Ge analyzers working at the Cu K-edge. Here, by perfecting each aspect of the fabrication, it is shown that spherically bent Si analyzers can provide the required energy resolution. Such analyzers have been successfully produced and have greatly improved the energy resolution in standard spherically bent analyzers.
TL;DR: The application of softer X-ray absorption spectroscopy to probe the local structural and electronic environment of metal ions within their biological complexes and during physiological reactions is discussed.
Abstract: Many inorganic species are now recognized as being essential for life, including many forms of sulfur, phosphate and numerous classes of metal ions. For example, recent progress in the fields of biochemistry and biology has pointed out the critical importance of sulfur in the biosynthesis of vital cofactors and active sites in proteins, and in the complex reaction mechanisms often involved. Special attention has also been drawn to the diverse roles of alkaline (Na(+), K(+)) and alkaline earth (Mg(2+), Ca(2+)) metal ions in mediating the activity of RNA, proteins and many processes in living cells. While the general effect of these ions in biology is mostly understood, information on their detailed role is deficient. Here the application of softer X-ray absorption spectroscopy (XAS) to probe the local structural and electronic environment of such ions within their biological complexes and during physiological reactions is discussed. In addition, the required experimental set-up and the difficulties associated with conducting softer XAS experiments on biological samples are presented.
TL;DR: The North West Structural Genomics Centre's beamline, MAD10, at the SRS receives the central part of the radiation fan produced by a new 2.46 T ten-pole wiggler, which enables screening of metals/Se in the crystal can be performed quickly prior to MAD/SAD data collection.
Abstract: The North West Structural Genomics Centre's beamline, MAD10, at the SRS receives the central part of the radiation fan (0.5 mrad vertically, 4 mrad horizontally) produced by a new 2.46 T ten-pole wiggler. The optical arrangement of the beamline consists of a Rh-coated collimating Si mirror, a fixed-exit-beam double-crystal monochromator with sagittal bending for horizontal focusing and a second Rh-coated Si mirror for vertical focusing. The double-crystal Si (111) monochromator allows data collection in the 5–13.5 keV photon energy range with rapid (subsecond) tunability and high energy resolution. The monochromatic beam is optimized through a 200 µm collimator. The beamline end station has been designed around a Mar desktop beamline with high-throughput cryogenic sample changer, Mar225 CCD detector, liquid-N2 autofill system and an ORTEC C-TRAIN-04 energy-resolving high-count-rate X-ray fluorescence detector. The instrument is optimized for MAD/SAD applications in protein crystallography with the additional mode of operation of online single-crystal EXAFS studies on the same crystals. Thus, screening of metals/Se in the crystal can be performed quickly prior to MAD/SAD data collection by exciting the crystal with X-rays of appropriate energy and recording an energy-dispersive fluorescence spectrum. In addition, this experimental set-up allows for parallel XAFS measurements on the same crystal to monitor `radiation-induced' changes, if any, in e.g. the redox state of metal centres to be detected for a `metallic' functional group during crystallographic data collection. Moreover, careful minimization of the thickness of the Be window maximizes the intensity performance for the 2.0–2.5 A softer wavelength range. This range also covers the K-edges of a number of important 3d transition metals as well as the L-edges of xenon and iodine and enhanced sulfur f ′′.
TL;DR: High-throughput X-ray absorption spectroscopy (HTXAS) is being developed as a technology for investigating the metalloproteome, with the promises and the pitfalls of HTXAS development, including the results of initial feasibility experiments.
Abstract: Structural and functional characterization of the entire protein complement (the proteome) of an organism can provide an infrastructure upon which questions about biological pathways and systems biology can be framed. The technology necessary to perform this proteome-level structural and functional characterization is under development in numerous structural genomics and functional genomics initiatives. Given the ubiquity of metal active sites in a proteome, it seems appropriate to ask whether comprehensive local structural characterization of metal sites within a proteome (metalloproteomics) is either a valid or obtainable goal. With a proteome-wide knowledge of the active-site structures of all metalloproteins, one could start to ask how metal insertion, cluster assembly and metalloprotein expression are affected by growth conditions or developmental status etc. High-throughput X-ray absorption spectroscopy (HTXAS) is being developed as a technology for investigating the metalloproteome. In creating a pipeline from genome to metalloproteome, several bottlenecks to high-throughput determination of metal-site structures must be overcome. For example, automation of arraying small samples for XAS examination must be invented, automation of rapid data collection of multiple low-volume low-concentration samples must be developed, automation of data reduction and analysis must be perfected. Discussed here are the promises and the pitfalls of HTXAS development, including the results of initial feasibility experiments.