On‐line optical and X‐ray spectroscopies with crystallography: an integrated approach for determining metalloprotein structures in functionally well defined states

X‐ray‐induced redox changes can lead to incorrect assignments of the functional states of metals in metalloprotein crystals. The need for on‐line monitoring of the status of metal ions (and other chromophores) during protein crystallography experiments is of growing importance with the use of intense synchrotron X‐ray beams. Significant efforts are therefore being made worldwide to combine different spectroscopies in parallel with X‐ray crystallographic data collection. Here the implementation and utilization of optical and X‐ray absorption spectroscopies on the modern macromolecular crystallography (MX) beamline 10, at the SRS, Daresbury Laboratory, is described. This beamline is equipped with a dedicated monolithic energy‐dispersive X‐ray fluorescence detector, allowing X‐ray absorption spectroscopy (XAS) measurements to be made in situ on the same crystal used to record the diffraction data. In addition, an optical microspectrophotometer has been incorporated on the beamline, thus facilitating combined MX, XAS and optical spectroscopic measurements. By uniting these techniques it is also possible to monitor the status of optically active and optically silent metal centres present in a crystal at the same time. This unique capability has been applied to observe the results of crystallographic data collection on crystals of nitrite reductase from Alcaligenes xylosoxidans, which contains both type‐1 and type‐2 Cu centres. It is found that the type‐1 Cu centre photoreduces quickly, resulting in the loss of the 595 nm peak in the optical spectrum, while the type‐2 Cu centre remains in the oxidized state over a much longer time period, for which independent confirmation is provided by XAS data as this centre has an optical spectrum which is barely detectable using microspectrophotometry. This example clearly demonstrates the importance of using two on‐line methods, spectroscopy and XAS, for identifying well defined redox states of metalloproteins during crystallographic data collection.     

X‐ray analog pixel array detector for single synchrotron bunch time‐resolved imaging

Dynamic X‐ray studies can reach temporal resolutions limited by only the X‐ray pulse duration if the detector is fast enough to segregate synchrotron pulses. An analog integrating pixel array detector with in‐pixel storage and temporal resolution of around 150 ns, sufficient to isolate pulses, is presented. Analog integration minimizes count‐rate limitations and in‐pixel storage captures successive pulses. Fundamental tests of noise and linearity as well as high‐speed laser measurements are shown. The detector resolved individual bunch trains at the Cornell High Energy Synchrotron Source at levels of up to 3.7 × 10³ X‐rays per pixel per train. When applied to turn‐by‐turn X‐ray beam characterization, single‐shot intensity measurements were made with a repeatability of 0.4% and horizontal oscillations of the positron cloud were detected.     

Radiation damage to protein specimens from electron beam imaging and diffraction: a mini‐review of anti‐damage approaches,with special reference to synchrotron X‐ray crystallography

Recent research progress using X‐ray cryo‐crystallography with the photon beams from third‐generation synchrotron sources has resulted in recognition that this intense radiation commonly damages protein samples even when they are held at 100 K. Other structural biologists examining thin protein crystals or single particle specimens encounter similar radiation damage problems during electron diffraction and imaging, but have developed some effective countermeasures. The aim of this concise review is to examine whether analogous approaches can be utilized to alleviate the X‐ray radiation damage problem in synchrotron macromolecular crystallography. The critical discussion of this question is preceded by presentation of background material on modern technical procedures with electron beam instruments using 300–400 kV accelerating voltage, low‐dose exposures for data recording, and protection of protein specimens by cryogenic cooling; these practical approaches to dealing with electron radiation damage currently permit best resolution levels of 6 Å (0.6 nm) for single particle specimens, and of 1.9 Å for two‐dimensional membrane protein crystals. Final determination of the potential effectiveness and practical value of using such new or unconventional ideas will necessitate showing, by experimental testing, that these produce significantly improved protection of three‐dimensional protein crystals during synchrotron X‐ray diffraction.     

In situ removal of carbon contamination from optics in a vacuum ultraviolet and soft X‐ray undulator beamline using oxygen activated by zeroth‐order synchrotron radiation

Carbon contamination of optics is a serious issue in all soft X‐ray beamlines because it decreases the quality of experimental data, such as near‐edge X‐ray absorption fine structure, resonant photoemission and resonant soft X‐ray emission spectra in the carbon K‐edge region. Here an in situ method involving the use of oxygen activated by zeroth‐order synchrotron radiation was used to clean the optics in a vacuum ultraviolet and soft X‐ray undulator beamline, BL‐13A at the Photon Factory in Tsukuba, Japan. The carbon contamination of the optics was removed by exposing them to oxygen at a pressure of 10^?1–10^?4 Pa for 17–20 h and simultaneously irradiating them with zeroth‐order synchrotron radiation. After the cleaning, the decrease in the photon intensity in the carbon K‐edge region reduced to 2–5%. The base pressure of the beamline recovered to 10^?7–10^?8 Pa in one day without baking. The beamline can be used without additional commissioning.     

Simple dose rate measurements for a very high synchrotron X‐ray flux

Dose measurements based on methylene blue (MB) bleaching, widely used for ultraviolet light, can also be applied to X‐rays including very high flux levels. This method has been tested by using both MB bleaching and Fricke dosimetry for a conventional monochromatic X‐ray source and then for `white‐beam' synchrotron radiation. The results show that MB bleaching dosimetry can easily measure X‐ray doses up to at least 10⁵ Gy s^?1, as long as the MB concentration is sufficiently high. This condition can be verified from the deviations from linearity of the bleaching versus exposure time.     

Sound velocities of compressed Fe3C from simultaneous synchrotron X‐ray diffraction and nuclear resonant scattering measurements

The applications of nuclear resonant scattering in laser‐heated diamond anvil cells have provided an important probe for the magnetic and vibrational properties of ⁵⁷Fe‐bearing materials under high pressure and high temperature. Synchrotron X‐ray diffraction is one of the most powerful tools for studying phase stability and equation of state over a wide range of pressure and temperature conditions. Recently an experimental capability has been developed for simultaneous nuclear resonant scattering and X‐ray diffraction measurements using synchrotron radiation. Here the application of this method to determine the sound velocities of compressed Fe₃C is shown. The X‐ray diffraction measurements allow detection of microscale impurities, phase transitions and chemical reactions upon compression or heating. They also provide information on sample pressure, grain size distribution and unit cell volume. By combining the Debye velocity extracted from the nuclear resonant inelastic X‐ray scattering measurements and the structure, density and elasticity data from the X‐ray diffraction measurements simultaneously obtained, more accurate sound velocity data can be derived. Our results on few‐crystal and powder samples indicate strong anisotropy in the sound velocities of Fe₃C under ambient conditions.     

Study of an archeological opaque red glass bead from China by XRD,XRF, and XANES

As a kind of rare archeological founding in China, red decorative beads (300–400 ad ) were discovered in Leijiaping, Badong County, Hubei, China. For the first time, this paper reports an advanced structural analysis of glass beads using micro synchrotron X‐ray near‐edge absorption spectroscopy. The results show that in spite of being opaque, the red bead is made of glass containing two forms of copper atoms, including 0⁺ and 1⁺. In combination with X‐ray diffraction results, it is advised that the mechanism of red coloration mainly comes from metallic copper. This paper indicates that micro synchrotron X‐ray near‐edge absorption spectroscopy is an outstanding and advanced technology to study ancient glass objects with nondestructive mode. Copyright © 2012 John Wiley & Sons, Ltd.     

BioCARS: a synchrotron resource for time‐resolved X‐ray science

BioCARS, a NIH‐supported national user facility for macromolecular time‐resolved X‐ray crystallography at the Advanced Photon Source (APS), has recently completed commissioning of an upgraded undulator‐based beamline optimized for single‐shot laser‐pump X‐ray‐probe measurements with time resolution as short as 100 ps. The source consists of two in‐line undulators with periods of 23 and 27 mm that together provide high‐flux pink‐beam capability at 12 keV as well as first‐harmonic coverage from 6.8 to 19 keV. A high‐heat‐load chopper reduces the average power load on downstream components, thereby preserving the surface figure of a Kirkpatrick–Baez mirror system capable of focusing the X‐ray beam to a spot size of 90 µm horizontal by 20 µm vertical. A high‐speed chopper isolates single X‐ray pulses at 1 kHz in both hybrid and 24‐bunch modes of the APS storage ring. In hybrid mode each isolated X‐ray pulse delivers up to ～4 × 10¹⁰ photons to the sample, thereby achieving a time‐averaged flux approaching that of fourth‐generation X‐FEL sources. A new high‐power picosecond laser system delivers pulses tunable over the wavelength range 450–2000 nm. These pulses are synchronized to the storage‐ring RF clock with long‐term stability better than 10 ps RMS. Monochromatic experimental capability with Biosafety Level 3 certification has been retained.     

A feasibility study of dynamic stress analysis inside a running internal combustion engine using synchrotron X‐ray beams

The present investigation establishes the feasibility of using synchrotron‐generated X‐ray beams for time‐resolved in situ imaging and diffraction of the interior components of an internal combustion engine during its operation. The demonstration experiment was carried out on beamline I12 (JEEP) at Diamond Light Source, UK. The external hutch of the JEEP instrument is a large‐scale engineering test bed for complex in situ processing and simulation experiments. The hutch incorporates a large capacity translation and rotation table and a selection of detectors for monochromatic and white‐beam diffraction and imaging. These capabilities were used to record X‐ray movies of a motorcycle internal combustion engine running at 1850 r.p.m. and to measure strain inside the connecting rod via stroboscopic X‐ray diffraction measurement. The high penetrating ability and high flux of the X‐ray beam at JEEP allowed the observation of inlet and outlet valve motion, as well as that of the piston, connecting rod and the timing chain within the engine. Finally, the dynamic internal strain within the moving connecting rod was evaluated with an accuracy of ～50 × 10^?6.     

Defect engineering by synchrotron radiation X‐rays in CeO2 nanocrystals

This work reports an unconventional defect engineering approach using synchrotron‐radiation‐based X‐rays on ceria nanocrystal catalysts of particle sizes 4.4–10.6 nm. The generation of a large number of oxygen‐vacancy defects (OVDs), and therefore an effective reduction of cations, has been found in CeO₂ catalytic materials bombarded by high‐intensity synchrotron X‐ray beams of beam size 1.5 mm × 0.5 mm, photon energies of 5.5–7.8 keV and photon fluxes up to 1.53 × 10¹² photons s^?1. The experimentally observed cation reduction was theoretically explained by a first‐principles formation‐energy calculation for oxygen vacancy defects. The results clearly indicate that OVD formation is mainly a result of X‐ray‐excited core holes that give rise to valence holes through electron down conversion in the material. Thermal annealing and subvalent Y‐doping were also employed to modulate the efficiency of oxygen escape, providing extra control on the X‐ray‐induced OVD generating process. Both the core‐hole‐dominated bond breaking and oxygen escape mechanisms play pivotal roles for efficient OVD formation. This X‐ray irradiation approach, as an alternative defect engineering method, can be applied to a wide variety of nanostructured materials for physical‐property modification.     

Guiding synchrotron X‐ray diffraction by multimodal video‐rate protein crystal imaging

Synchronous digitization, in which an optical sensor is probed synchronously with the firing of an ultrafast laser, was integrated into an optical imaging station for macromolecular crystal positioning prior to synchrotron X‐ray diffraction. Using the synchronous digitization instrument, second‐harmonic generation, two‐photon‐excited fluorescence and bright field by laser transmittance were all acquired simultaneously with perfect image registry at up to video‐rate (15 frames s^?1). A simple change in the incident wavelength enabled simultaneous imaging by two‐photon‐excited ultraviolet fluorescence, one‐photon‐excited visible fluorescence and laser transmittance. Development of an analytical model for the signal‐to‐noise enhancement afforded by synchronous digitization suggests a 15.6‐fold improvement over previous photon‐counting techniques. This improvement in turn allowed acquisition on nearly an order of magnitude more pixels than the preceding generation of instrumentation and reductions of well over an order of magnitude in image acquisition times. These improvements have allowed detection of protein crystals on the order of 1 µm in thickness under cryogenic conditions in the beamline. These capabilities are well suited to support serial crystallography of crystals approaching 1 µm or less in dimension.     

Influence of crystallographic orientation of biogenic calcite on in situ Mg XANES analyses

Micro X‐ray absorption near‐edge spectroscopy at the Mg K‐edge is a useful technique for acquiring information about the environment of Mg²⁺ in biogenic calcite. These analyses can be applied to shell powders or intact shell structures. The advantage of the latter is that the XANES analyses can be applied to specific areas, at high (e.g. micrometre) spatial resolution, to determine the environment of Mg²⁺ in a biomineral context. Such in situ synchrotron analysis has to take into account the potential effect of crystallographic orientation given the anisotropy of calcite crystals and the polarized nature of X‐rays. Brachiopod shells of species with different crystallographic orientations are used to assess this crystallographic effect on in situ synchrotron measurements at the Mg K‐edge. Results show that, owing to the anisotropy of calcite, in situ X‐ray absorption spectra (XAS) are influenced by the crystallographic orientation of calcite crystals with a subsequent potentially erroneous interpretation of Mg²⁺ data. Thus, this study demonstrates the importance of crystallography for XAS analyses and, therefore, the necessity to obtain crystallographic information at high spatial resolution prior to spectroscopic analysis.     

Structural variation in a synchrotron‐induced contamination layer (a‐C:H) deposited on a toroidal Au mirror surface

A carbon layer deposited on an optical component is the result of complex interactions between the optical surface, adsorbed hydrocarbons, photons and secondary electrons (photoelectrons generated on the surface of optical elements). In the present study a synchrotron‐induced contamination layer on a 340 mm × 60 mm Au‐coated toroidal mirror has been characterized. The contamination layer showed a strong variation in structural properties from the centre of the mirror to the edge region (along the long dimension of the mirror) due to the Gaussian distribution of the incident photon beam intensity/power on the mirror surface. Raman scattering measurements were carried out at 12 equidistant (25 mm) locations along the length of the mirror. The surface contamination layer that formed on the Au surface was observed to be hydrogenated amorphous carbon film in nature. The effects of the synchrotron beam intensity/power distribution on the structural properties of the contamination layer are discussed. The I(D)/I(G) ratio, cluster size and disordering were found to increase whereas the sp²:sp³ ratio, G peak position and H content decreased with photon dose. The structural parameters of the contamination layer in the central region were estimated (thickness ? 400 Å, roughness ? 60 Å, density ? 72% of bulk graphitic carbon density) by soft X‐ray reflectivity measurements. The amorphous nature of the layer in the central region was observed by grazing‐incidence X‐ray diffraction.     

Implementation of ultrafast X‐ray diffraction at the 1W2B wiggler beamline of Beijing Synchrotron Radiation Facility

The implementation of a laser pump/X‐ray probe scheme for performing picosecond‐resolution X‐ray diffraction at the 1W2B wiggler beamline at Beijing Synchrotron Radiation Facility is reported. With the hybrid fill pattern in top‐up mode, a pixel array X‐ray detector was optimized to gate out the signal from the singlet bunch with interval 85 ns from the bunch train. The singlet pulse intensity is ～2.5 × 10⁶ photons pulse^?1 at 10 keV. The laser pulse is synchronized to this singlet bunch at a 1 kHz repetition rate. A polycapillary X‐ray lens was used for secondary focusing to obtain a 72 µm (FWHM) X‐ray spot. Transient photo‐induced strain in BiFeO₃ film was observed at a ～150 ps time resolution for demonstration.     

Single‐cell resolution in high‐resolution synchrotron X‐ray CT imaging with gold nanoparticles

Gold nanoparticles are excellent intracellular markers in X‐ray imaging. Having shown previously the suitability of gold nanoparticles to detect small groups of cells with the synchrotron‐based computed tomography (CT) technique both ex vivo and in vivo, it is now demonstrated that even single‐cell resolution can be obtained in the brain at least ex vivo. Working in a small animal model of malignant brain tumour, the image quality obtained with different imaging modalities was compared. To generate the brain tumour, 1 × 10⁵ C6 glioma cells were loaded with gold nanoparticles and implanted in the right cerebral hemisphere of an adult rat. Raw data were acquired with absorption X‐ray CT followed by a local tomography technique based on synchrotron X‐ray absorption yielding single‐cell resolution. The reconstructed synchrotron X‐ray images were compared with images obtained by small animal magnetic resonance imaging. The presence of gold nanoparticles in the tumour tissue was verified in histological sections.     

Diffraction‐based automated crystal centering

A fully automated procedure for detecting and centering protein crystals in the X‐ray beam of a macromolecular crystallography beamline has been developed. A cryo‐loop centering routine that analyzes video images with an edge detection algorithm is first used to determine the dimensions of the loop holding the sample; then low‐dose X‐rays are used to record diffraction images in a grid over the edge and face plane of the loop. A three‐dimensional profile of the crystal based on the number of diffraction spots in each image is constructed. The derived center of mass is then used to align the crystal to the X‐ray beam. Typical samples can be accurately aligned in ～2–3 min. Because the procedure is based on the number of `good' spots as determined by the program Spotfinder, the best diffracting part of the crystal is aligned to the X‐ray beam.     

Ultra‐thin optical grade scCVD diamond as X‐ray beam position monitor

Results of measurements made at the SIRIUS beamline of the SOLEIL synchrotron for a new X‐ray beam position monitor based on a super‐thin single crystal of diamond grown by chemical vapor deposition (CVD) are presented. This detector is a quadrant electrode design processed on a 3 µm‐thick membrane obtained by argon–oxygen plasma etching the central area of a CVD‐grown diamond plate of 60 µm thickness. The membrane transmits more than 50% of the incident 1.3 keV energy X‐ray beam. The diamond plate was of moderate purity (～1 p.p.m. nitrogen), but the X‐ray beam induced current (XBIC) measurements nevertheless showed a photo‐charge collection efficiency approaching 100% for an electric field of 2 V µm^?1, corresponding to an applied bias voltage of only 6 V. XBIC mapping of the membrane showed an inhomogeneity of more than 10% across the membrane, corresponding to the measured variation in the thickness of the diamond plate before the plasma etching process. The measured XBIC signal‐to‐dark‐current ratio of the device was greater than 10⁵, and the X‐ray beam position resolution of the device was better than a micrometer for a 1 kHz sampling rate.     

Pressure study of monoclinic ReO2 up to 1.2 GPa using X‐ray absorption spectroscopy and X‐ray diffraction

The crystal and local atomic structure of monoclinic ReO₂ (α‐ReO₂) under hydrostatic pressure up to 1.2 GPa was investigated for the first time using both X‐ray absorption spectroscopy and high‐resolution synchrotron X‐ray powder diffraction and a home‐built B₄C anvil pressure cell developed for this purpose. Extended X‐ray absorption fine‐structure (EXAFS) data analysis at pressures from ambient up to 1.2 GPa indicates that there are two distinct Re—Re distances and a distorted ReO₆ octahedron in the α‐ReO₂ structure. X‐ray diffraction analysis at ambient pressure revealed an unambiguous solution for the crystal structure of the α‐phase, demonstrating a modulation of the Re—Re distances. The relatively small portion of the diffraction pattern accessed in the pressure‐dependent measurements does not allow for a detailed study of the crystal structure of α‐ReO₂ under pressure. Nonetheless, a shift and reduction in the (011) Bragg peak intensity between 0.4 and 1.2 GPa is observed, with correlation to a decrease in Re—Re distance modulation, as confirmed by EXAFS analysis in the same pressure range. This behavior reveals that α‐ReO₂ is a possible inner pressure gauge for future experiments up to 1.2 GPa.     

Diamond X‐ray beam‐position monitoring using signal readout at the synchrotron radiofrequency

Single‐crystal diamond is a material with great potential for the fabrication of X‐ray photon beam‐position monitors with submicrometre spatial resolution. Low X‐ray absorption combined with radiation hardness and excellent thermal‐mechanical properties make possible beam‐transmissive diamond devices for monitoring synchrotron and free‐electron laser X‐ray beams. Tests were made using a white bending‐magnet synchrotron X‐ray beam at DESY to investigate the performance of a position‐sensitive diamond device using radiofrequency readout electronics. The device uniformity and position response were measured in a 25 µm collimated X‐ray beam with an I‐Tech Libera `Brilliance' system. This readout system was designed for position measurement and feedback control of the electron beam in the synchrotron storage ring, but, as shown here, it can also be used for accurate position readout of a quadrant‐electrode single‐crystal diamond sensor. The centre‐of‐gravity position of the F4 X‐ray beam at the DORIS III synchrotron was measured with the diamond signal output digitally sampled at a rate of 130 Msample s^?1 by the Brilliance system. Narrow‐band filtering and digital averaging of the position signals resulted in a measured position noise below 50 nm (r.m.s.) for a 10 Hz bandwidth.