XDS: a flexible beamline for X‐ray diffraction and spectroscopy at the Brazilian synchrotron

The majority of the beamlines at the Brazilian Synchrotron Light Source Laboratory (LNLS) use radiation produced in the storage‐ring bending magnets and are therefore currently limited in the flux that can be used in the harder part of the X‐ray spectrum (above ～10 keV). A 4 T superconducting multipolar wiggler (SCW) was recently installed at LNLS in order to improve the photon flux above 10 keV and fulfill the demands set by the materials science community. A new multi‐purpose beamline was then installed at the LNLS using the SCW as a photon source. The XDS is a flexible beamline operating in the energy range between 5 and 30 keV, designed to perform experiments using absorption, diffraction and scattering techniques. Most of the work performed at the XDS beamline concentrates on X‐ray absorption spectroscopy at energies above 18 keV and high‐resolution diffraction experiments. More recently, new setups and photon‐hungry experiments such as total X‐ray scattering, X‐ray diffraction under high pressures, resonant X‐ray emission spectroscopy, among others, have started to become routine at XDS. Here, the XDS beamline characteristics, performance and a few new experimental possibilities are described.     

ALBA Synchrotron Facility

ALBA is the Spanish synchrotron facility located in the area of Barcelona. It is a low-emittance, 3 GeV machine having, at present, seven state-of-the-art operating beamlines covering soft and hard X-rays. The hard X-ray beamlines comprise macromolecular crystallography, non-crystalline diffraction (SAXS and WAXS), high-resolution powder diffraction, and absorption spectroscopy. The soft X-ray beamlines include a photoemission beamline with two endstations—one devoted to photoelectron microscopy (PEEM) and the second to near ambient pressure photoemission (NAPP)—and another beamline devoted to XMCD and soft X-ray scattering. Both beamlines allow full control of the polarization of the beam, since they are equipped with helical undulators. An additional soft X-ray beamline, installed on a bending magnet port, is equipped with a full-field transmission X-ray microscope. Additional information may be found at http://www.albasynchrotron.es/en/beamlines.     

The multi‐purpose hard X‐ray beamline BL10 at the DELTA storage ring

The layout and the characteristics of the hard X‐ray beamline BL10 at the superconducting asymmetric wiggler at the 1.5 GeV Dortmund Electron Accelerator DELTA are described. This beamline is equipped with a Si(111) channel‐cut monochromator and is dedicated to X‐ray studies in the spectral range from ～4 keV to ～16 keV photon energy. There are two different endstations available. While X‐ray absorption studies in different detection modes (transmission, fluorescence, reflectivity) can be performed on a designated table, a six‐axis kappa diffractometer is installed for X‐ray scattering and reflectivity experiments. Different detector set‐ups are integrated into the beamline control software, i.e. gas‐filled ionization chambers, different photodiodes, as well as a Pilatus 2D‐detector are permanently available. The performance of the beamline is illustrated by high‐quality X‐ray absorption spectra from several reference compounds. First applications include temperature‐dependent EXAFS experiments from liquid‐nitrogen temperature in a bath cryostat up to ～660 K by using a dedicated furnace. Besides transmission measurements, fluorescence detection for dilute sample systems as well as surface‐sensitive reflection‐mode experiments are presented.     

Protein crystallography beamline (PX‐BL21) at Indus‐2 synchrotron

The protein crystallography beamline (PX‐BL21), installed at the 1.5 T bending‐magnet port at the Indian synchrotron (Indus‐2), is now available to users. The beamline can be used for X‐ray diffraction measurements on a single crystal of macromolecules such as proteins, nucleic acids and their complexes. PX‐BL21 has a working energy range of 5–20 keV for accessing the absorption edges of heavy elements commonly used for phasing. A double‐crystal monochromator [Si(111) and Si(220)] and a pair of rhodium‐coated X‐ray mirrors are used for beam monochromatization and manipulation, respectively. This beamline is equipped with a single‐axis goniometer, Rayonix MX225 CCD detector, fluorescence detector, cryogenic sample cooler and automated sample changer. Additional user facilities include a workstation for on‐site data processing and a biochemistry laboratory for sample preparation. In this article the beamline, other facilities and some recent scientific results are briefly described.     

The materials science X‐ray beamline BL8 at the DELTA storage ring

The hard X‐ray beamline BL8 at the superconducting asymmetric wiggler at the 1.5 GeV Dortmund Electron Accelerator DELTA is described. This beamline is dedicated to X‐ray studies in the spectral range from ～1 keV to ～25 keV photon energy. The monochromator as well as the other optical components of the beamline are optimized accordingly. The endstation comprises a six‐axis diffractometer that is capable of carrying heavy loads related to non‐ambient sample environments such as, for example, ultrahigh‐vacuum systems, high‐pressure cells or liquid‐helium cryostats. X‐ray absorption spectra from several reference compounds illustrate the performance. Besides transmission measurements, fluorescence detection for dilute sample systems as well as surface‐sensitive reflection‐mode experiments have been performed. The results show that high‐quality EXAFS data can be obtained in the quick‐scanning EXAFS mode within a few seconds of acquisition time, enabling time‐resolved in situ experiments using standard beamline equipment that is permanently available. The performance of the new beamline, especially in terms of the photon flux and energy resolution, is competitive with other insertion‐device beamlines worldwide, and several sophisticated experiments including surface‐sensitive EXAFS experiments are feasible.     

Investigations of mechanical vibrations for beamlines at the Canadian Light Source

Vibration is often a problem causing poor quality of photon beams at synchrotron radiation facilities, since beamlines are quite sensitive to vibrations. Therefore, vibration analysis and control at synchrotron radiation facilities is crucial. This paper presents investigations on mechanical vibrations at four beamlines and endstations at the Canadian Light Source, i.e. the Canadian Macromolecular Crystallography Facility 08ID‐1 beamline, the Hard X‐ray MicroAnalysis 06ID‐1 beamline, the Resonant Elastic and Inelastic Soft X‐ray Scattering 10ID‐2 beamline, and the Scanning Transmission X‐ray Microscope endstation at the Spectromicroscopy 10ID‐1 beamline. This study identifies vibration sources and investigates the influence of mechanical vibrations on beamline performance. The results show that vibrations caused by movable mechanical equipment significantly affect the data acquired from beamlines.     

A comparative study of the spectra recorded at RRCAT synchrotron BL-8 dispersive EXAFS beamline with other beamlines

The aim of the present work is to make a comparative study of the EXAFS spectra recorded at the BL-8 dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at RRCAT, Indore (India) with those recorded at other synchrotron EXAFS beamlines, viz., X-19A at NSLS, BNL (USA), EXAFS wiggler beamline 4-1 at the SSRL (USA) and beamline 11.1 at ELETTRA (Italy). For this purpose, EXAFS spectra at Cu K-edge in copper metal have been recorded at these four beamlines. Further, EXAFS spectra at Cu K-edge in a copper complex have also been recorded at BL-8 beamline and beamline 11.1 at ELETTRA (Italy). The obtained experimental μ(E) data have been background-subtracted and then normalized. The normalized data have been then converted to χ(k) data, which have been Fourier-transformed and then fitted with the theoretical model, thereby yielding different structural parameters. It has been shown that the results obtained from the EXAFS spectra recorded at the BL-8 beamline are comparable with those obtained from other synchrotron EXAFS beamlines and also with the crystallographic results reported by earlier workers. The reliability, usefulness and data quality of the BL-8 beamline have been discussed.     

Beamline AR‐NW12A: high‐throughput beamline for macromolecular crystallography at the Photon Factory

AR‐NW12A is an in‐vacuum undulator beamline optimized for high‐throughput macromolecular crystallography experiments as one of the five macromolecular crystallography (MX) beamlines at the Photon Factory. This report provides details of the beamline design, covering its optical specifications, hardware set‐up, control software, and the latest developments for MX experiments. The experimental environment presents state‐of‐the‐art instrumentation for high‐throughput projects with a high‐precision goniometer with an adaptable goniometer head, and a UV‐light sample visualization system. Combined with an efficient automounting robot modified from the SSRL SAM system, a remote control system enables fully automated and remote‐access X‐ray diffraction experiments.     

Characterization of an in‐vacuum PILATUS 1M detector

A dedicated in‐vacuum X‐ray detector based on the hybrid pixel PILATUS 1M detector has been installed at the four‐crystal monochromator beamline of the PTB at the electron storage ring BESSY II in Berlin, Germany. Owing to its windowless operation, the detector can be used in the entire photon energy range of the beamline from 10 keV down to 1.75 keV for small‐angle X‐ray scattering (SAXS) experiments and anomalous SAXS at absorption edges of light elements. The radiometric and geometric properties of the detector such as quantum efficiency, pixel pitch and module alignment have been determined with low uncertainties. The first grazing‐incidence SAXS results demonstrate the superior resolution in momentum transfer achievable at low photon energies.     

Automatic crystal centring procedure at the SSRF macromolecular crystallography beamline

X‐ray diffraction is a common technique for determining crystal structures. The average time needed for the solution of a protein structure has been drastically reduced by a number of recent experimental and theoretical developments. Since high‐throughput protein crystallography benefits from full automation of all steps that are carried out on a synchrotron beamline, an automatic crystal centring procedure is important for crystallographic beamlines. Fully automatic crystal alignment involves the application of optical methods to identify the crystal and move it onto the rotation axis and into the X‐ray beam. Crystal recognition has complex dependencies on the illumination, crystal size and viewing angles due to effects such as local shading, inter‐reflections and the presence of antifreezing elements. Here, a rapid procedure for crystal centring with multiple cameras using region segment thresholding is reported. Firstly, a simple illumination‐invariant loop recognition and classification model is used by slicing a low‐magnification loop image into small region segments, then classifying the loop into different types and aligning it to the beam position using feature vectors of the region segments. Secondly, an edge detection algorithm is used to find the crystal sample in a high‐magnification image using region segment thresholding. Results show that this crystal centring method is extremely successful under fluctuating light states as well as for poorly frozen and opaque samples. Moreover, this crystal centring procedure is successfully integrated into the enhanced Blu‐Ice data collection system at beamline BL17U1 at the Shanghai Synchrotron Radiation Facility as a routine method for an automatic crystal screening procedure.     

Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography

The sulfur SAD phasing method allows the determination of protein structures de novo without reference to derivatives such as Se‐methionine. The feasibility for routine automated sulfur SAD phasing using a number of current protein crystallography beamlines at several synchrotrons was examined using crystals of trimeric Achromobacter cycloclastes nitrite reductase (AcNiR), which contains a near average proportion of sulfur‐containing residues and two Cu atoms per subunit. Experiments using X‐ray wavelengths in the range 1.9–2.4 Å show that we are not yet at the level where sulfur SAD is routinely successful for automated structure solution and model building using existing beamlines and current software tools. On the other hand, experiments using the shortest X‐ray wavelengths available on existing beamlines could be routinely exploited to solve and produce unbiased structural models using the similarly weak anomalous scattering signals from the intrinsic metal atoms in proteins. The comparison of long‐wavelength phasing (the Bijvoet ratio for nine S atoms and two Cu atoms is ～1.25% at ～2 Å) and copper phasing (the Bijvoet ratio for two Cu atoms is 0.81% at ～0.75 Å) for AcNiR suggests that lower data multiplicity than is currently required for success should in general be possible for sulfur phasing if appropriate improvements to beamlines and data collection strategies can be implemented.     

Attosecond laser station

The attosecond laser station(ALS) at the Synergetic Extreme Condition User Facility(SECUF) is a sophisticated and user-friendly platform for the investigation of the electron dynamics in atoms, molecules, and condensed matter on timescales ranging from tens of femtoseconds to tens of attoseconds. Short and tunable coherent extreme-ultraviolet(XUV)light sources based on high-order harmonic generation in atomic gases are being developed to drive a variety of endstations for inspecting and controlling ultrafast electron dynamics in real time. The combination of such light sources and end-stations offers a route to investigate fundamental physical processes in atoms, molecules, and condensed matter. The ALS consists of four beamlines, each containing a light source designed specifically for application experiments that will be performed in its own end-station. The first beamline will produce broadband XUV light for attosecond photoelectron spectroscopy and attosecond transient absorption spectroscopy. It is also capable of performing attosecond streaking to characterize isolated attosecond pulses and will allow studies on the electron dynamics in atoms, moleculars, and condensed matter. The second XUV beamline will produce narrowband femtosecond XUV pulses for time-resolved and angle-resolved photoelectron spectroscopy, to study the electronic dynamics on the timescale of fundamental correlations and interactions in solids, especially in superconductors and topological insulators. The third beamline will produce broadband XUV pulses for attosecond coincidence spectroscopy in a cold-target recoil-ion momentum spectrometer, to study the ultrafast dynamics and reactions in atomic and molecular systems. The last beamline produces broadband attosecond XUV pulses designed for time-resolved photoemission electron microscopy, to study the ultrafast dynamics of plasmons in nanostructures and the surfaces of solid materials with high temporal and spatial resolutions simultaneously. The main object of the ALS is to provide domestic and international scientists with unique tools to study fundamental processes in physics, chemistry,biology, and material sciences with ultrafast temporal resolutions on the atomic scale.     

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.     

Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system

Biological small-angle X-ray scattering (SAXS) provides powerful complementary data for macromolecular crystallography (MX) by defining shape, conformation and assembly in solution. Although SAXS is in principle the highest throughput technique for structural biology, data collection is limited in practice by current data collection software. Here the adaption of beamline control software, historically developed for MX beamlines, for the efficient operation and high-throughput data collection at synchrotron SAXS beamlines is reported. The Blu-Ice GUI and Distributed Control System (DCS) developed in the Macromolecular Crystallography Group at the Stanford Synchrotron Radiation Laboratory has been optimized, extended and enhanced to suit the specific needs of the biological SAXS endstation at the SIBYLS beamline at the Advanced Light Source. The customizations reported here provide a potential route for other SAXS beamlines in need of robust and efficient beamline control software. As a great deal of effort and optimization has gone into crystallographic software, the adaption and extension of crystallographic software may prove to be a general strategy to provide advanced SAXS software for the synchrotron community. In this way effort can be put into optimizing features for SAXS rather than reproducing those that have already been successfully implemented for the crystallographic community.     

Microcrystallography using single‐bounce monocapillary optics

X‐ray microbeams have become increasingly valuable in protein crystallography. A number of synchrotron beamlines worldwide have adapted to handling smaller and more challenging samples by providing a combination of high‐precision sample‐positioning hardware, special visible‐light optics for sample visualization, and small‐diameter X‐ray beams with low background scatter. Most commonly, X‐ray microbeams with diameters ranging from 50 µm to 1 µm are produced by Kirkpatrick and Baez mirrors in combination with defining apertures and scatter guards. A simple alternative based on single‐bounce glass monocapillary X‐ray optics is presented. The basic capillary design considerations are discussed and a practical and robust implementation that capitalizes on existing beamline hardware is presented. A design for mounting the capillary is presented which eliminates parasitic scattering and reduces deformations of the optic to a degree suitable for use on next‐generation X‐ray sources. Comparison of diffraction data statistics for microcrystals using microbeam and conventional aperture‐collimated beam shows that capillary‐focused beam can deliver significant improvement. Statistics also confirm that the annular beam profile produced by the capillary optic does not impact data quality in an observable way. Examples are given of new structures recently solved using this technology. Single‐bounce monocapillary optics can offer an attractive alternative for retrofitting existing beamlines for microcrystallography.     

Obtaining local reciprocal lattice vectors from finite‐element analysis

Finite‐element analysis is frequently used by engineers at synchrotron beamlines to calculate the elastic deformation of a single crystal undergoing mechanical bending or thermal load. ANSYS^® Workbench? software is widely used for such simulations. However, although ANSYS^® Workbench? software provides useful information on the displacements, strains and stresses within the crystal, it does not yield the local reciprocal lattice vectors that would be required for X‐ray diffraction calculations. To bridge this gap, a method based on the shape functions and interpolation procedures of the software itself has been developed. An application to the double‐crystal bent Laue monochromator being designed for the I12 (JEEP) wiggler beamline at the Diamond Light Source is presented.