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.     

DISCO synchrotron‐radiation circular‐dichroism endstation at SOLEIL

The new synchrotron‐radiation circular‐dichroism (SRCD) endstation on the UV‐visible synchrotron beamline DISCO has been commissioned at the SOLEIL synchrotron. The design has been focused on preservation of a high degree of linear polarization at high flux and moderate resolving power covering the vacuum ultraviolet to visible spectral range (125–600 nm). The beam dimensions have been set to 4 mm × 4 mm at 1 nm bandwidth for lower sample degradation. The nitrogen‐purged sample chamber fits three types of sample holders accommodating conventional round cell mounting, automated rotation of the samples, as well as a microfluidic set‐up. Automated temperature‐controlled data collection on microvolumes is now available to the biology and chemistry communities. Macromolecules including membrane proteins, soluble proteins, bio‐nanotubes, sugars, DNA and RNAs are now routinely investigated.     

Multi‐use high/low‐temperature and pressure compatible portable chamber for in situ grazing‐incidence X‐ray scattering studies

The multipurpose portable ultra‐high‐vacuum‐compatible chamber described in detail in this article has been designed to carry out grazing‐incidence X‐ray scattering techniques on the BM25‐SpLine CRG beamline at the ESRF. The chamber has a cylindrical form, built on a 360° beryllium double‐ended conflate flange (CF) nipple. The main advantage of this chamber design is the wide sample temperature range, which may be varied between 60 and 1000 K. Other advantages of using a cylinder are that the wall thickness is reduced to a minimum value, keeping maximal solid angle accessibility and keeping wall absorption of the incoming X‐ray beam constant. The heat exchanger is a customized compact liquid‐nitrogen (LN2) continuous‐flow cryostat. LN2 is transferred from a storage Dewar through a vacuum‐isolated transfer line to the heat exchanger. The sample is mounted on a molybdenum support on the heat exchanger, which is equipped with a BORALECTRIC heater element. The chamber versatility extends to the operating pressure, ranging from ultra‐high vacuum (<10^?10 mbar) to high pressure (up to 3 × 10³ mbar). In addition, it is equipped with several CF ports to allocate auxiliary components such as capillary gas‐inlet, viewports, leak valves, ion gun, turbo pump, etc., responding to a large variety of experiment requirements. A movable slits set‐up has been foreseen to reduce the background and diffuse scattering produced at the beryllium wall. Diffraction data can be recorded either with a point detector or with a bi‐dimensional CCD detector, or both detectors simultaneously. The system has been designed to carry out a multitude of experiments in a large variety of environments. The system feasibility is demonstrated by showing temperature‐dependence grazing‐incidence X‐ray diffraction and conductivity measurements on a 20 nm‐thick La_0.7Ca_0.3MnO₃ thin film grown on a SrTiO₃(001) substrate.     

A setup for synchrotron‐radiation‐induced total reflection X‐ray fluorescence and X‐ray absorption near‐edge structure recently commissioned at BESSY II BAMline

An automatic sample changer chamber for total reflection X‐ray fluorescence (TXRF) and X‐ray absorption near‐edge structure (XANES) analysis in TXRF geometry was successfully set up at the BAMline at BESSY II. TXRF and TXRF‐XANES are valuable tools for elemental determination and speciation, especially where sample amounts are limited (<1 mg) and concentrations are low (ng ml^?1 to µg ml^?1). TXRF requires a well defined geometry regarding the reflecting surface of a sample carrier and the synchrotron beam. The newly installed chamber allows for reliable sample positioning, remote sample changing and evacuation of the fluorescence beam path. The chamber was successfully used showing accurate determination of elemental amounts in the certified reference material NIST water 1640. Low limits of detection of less than 100 fg absolute (10 pg ml^?1) for Ni were found. TXRF‐XANES on different Re species was applied. An unknown species of Re was found to be Re in the +7 oxidation state.     

IDATEN and G‐SITENNO: GUI‐assisted software for coherent X‐ray diffraction imaging experiments and data analyses at SACLA

Using our custom‐made diffraction apparatus KOTOBUKI‐1 and two multiport CCD detectors, cryogenic coherent X‐ray diffraction imaging experiments have been undertaken at the SPring‐8 Angstrom Compact free electron LAser (SACLA) facility. To efficiently perform experiments and data processing, two software suites with user‐friendly graphical user interfaces have been developed. The first is a program suite named IDATEN, which was developed to easily conduct four procedures during experiments: aligning KOTOBUKI‐1, loading a flash‐cooled sample into the cryogenic goniometer stage inside the vacuum chamber of KOTOBUKI‐1, adjusting the sample position with respect to the X‐ray beam using a pair of telescopes, and collecting diffraction data by raster scanning the sample with X‐ray pulses. Named G‐SITENNO, the other suite is an automated version of the original SITENNO suite, which was designed for processing diffraction data. These user‐friendly software suites are now indispensable for collecting a large number of diffraction patterns and for processing the diffraction patterns immediately after collecting data within a limited beam time.     

Femtosecond laser microstructuring: an enabling tool for optofluidic lab‐on‐chips

This paper provides an overview of the rather new field concerning the applications of femtosecond laser microstructuring of glass to optofluidics. Femtosecond lasers have recently emerged as a powerful microfabrication tool due to their unique characteristics. On the one hand, they enable to induce a permanent refractive index increase, in a micrometer‐sized volume of the material, allowing single‐step, three‐dimensional fabrication of optical waveguides. On the other hand, femtosecond‐laser irradiation of fused silica followed by chemical etching enables the manufacturing of directly buried microfluidic channels. This opens the intriguing possibility of using a single laser system for the fabrication and three‐dimensional integration of optofluidic devices. This paper will review the state of the art of femtosecond laser fabrication of optical waveguides and microfluidic channels, as well as their integration for high sensitivity detection of biomolecules and for cell manipulation.     

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 new small‐angle X‐ray scattering set‐up on the crystallography beamline I711 at MAX‐lab

A small‐angle X‐ray scattering (SAXS) set‐up has recently been developed at beamline I711 at the MAX II storage ring in Lund (Sweden). An overview of the required modifications is presented here together with a number of application examples. The accessible q range in a SAXS experiment is 0.009–0.3 Å^?1 for the standard set‐up but depends on the sample‐to‐detector distance, detector offset, beamstop size and wavelength. The SAXS camera has been designed to have a low background and has three collinear slit sets for collimating the incident beam. The standard beam size is about 0.37 mm × 0.37 mm (full width at half‐maximum) at the sample position, with a flux of 4 × 10¹⁰ photons s^?1 and λ = 1.1 Å. The vacuum is of the order of 0.05 mbar in the unbroken beam path from the first slits until the exit window in front of the detector. A large sample chamber with a number of lead‐throughs allows different sample environments to be mounted. This station is used for measurements on weakly scattering proteins in solutions and also for colloids, polymers and other nanoscale structures. A special application supported by the beamline is the effort to establish a micro‐fluidic sample environment for structural analysis of samples that are only available in limited quantities. Overall, this work demonstrates how a cost‐effective SAXS station can be constructed on a multipurpose beamline.     

I19, the small‐molecule single‐crystal diffraction beamline at Diamond Light Source

The dedicated small‐molecule single‐crystal X‐ray diffraction beamline (I19) at Diamond Light Source has been operational and supporting users for over three years. I19 is a high‐flux tunable‐wavelength beamline and its key details are described in this article. Much of the work performed on the beamline involves structure determination from small and weakly diffracting crystals. Other experiments that have been supported to date include structural studies at high pressure, studies of metastable species, variable‐temperature crystallography, studies involving gas exchange in porous materials and structural characterizations that require analysis of the diffuse scattering between Bragg reflections. A range of sample environments to facilitate crystallographic studies under non‐ambient conditions are available as well as a number of options for automation. An indication of the scope of the science carried out on the beamline is provided by the range of highlights selected for this paper.     

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.     

Raman‐induced impulsive Stokes lasing in novel SRS‐active monoclinic m‐LaVO4 crystal

Monoclinic m‐LaVO₄ vanadate with the monazite‐type structure was found to be a new favorable SRS‐active crystal. Its two‐phonon impulsive Stokes lasing has been recorded under near‐IR femtosecond pumping. Knowledge acquired about the behavior of impulsive stimulated Raman scattering in the studied crystals may be useful for the physics of coherent optical phonons and for engineering of femtosecond lasers. The fundamental results obtained here will also motivate the search for crystals able to generate multiphonon impulsive SRS. (© 2015 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

A 3 × 6 arrayed CCD X‐ray detector for continuous rotation method in macromolecular crystallography

A 3 × 6 arrayed charge‐coupled device (CCD) X‐ray detector has been developed for the continuous‐rotation method in macromolecular crystallography at the Photon Factory. The detector has an area of 235.9 mm × 235.9 mm and a readout time of 1.9 s. The detector is made of a 3 × 6 array of identical modules, each module consisting of a fiber‐optic taper (FOT), a CCD sensor and a readout circuit. The outputs from 18 CCDs are read out in parallel and are then digitized by 16‐bit analog‐to‐digital converters. The advantage of this detector over conventional FOT‐coupled CCD detectors is the unique CCD readout scheme (frame transfer) which enables successive X‐ray exposures to be recorded without interruption of the sample crystal rotation. A full data set of a lysozyme crystal was continuously collected within 360 s (180° rotation, 3 s/1.5° frame). The duty‐cycle ratio of the X‐ray exposure to the data collection time was almost 100%. The combination of this detector and synchrotron radiation is well suited to rapid and continuous data collection in macromolecular crystallography.     

SOLEIL shining on the solution‐state structure of biomacromolecules by synchrotron X‐ray footprinting at the Metrology beamline

Synchrotron X‐ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small‐angle X‐ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X‐ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France. This work presents X‐ray footprinting of biomolecules performed for the first time at the X‐ray Metrology beamline at the SOLEIL synchrotron radiation source. The installation at this beamline of a stopped‐flow apparatus for sample delivery, an irradiation capillary and an automatic sample collector enabled the X‐ray footprinting study of the structure of the soluble protein factor H (FH) from the human complement system as well as of the lipid‐associated hydrophobic protein S3 oleosin from plant seed. Mass spectrometry analysis showed that the structural integrity of both proteins was not affected by the short exposition to the oxygen radicals produced during the irradiation. Irradiated molecules were subsequently analysed using high‐resolution mass spectrometry to identify and locate oxidized amino acids. Moreover, the analyses of FH in its free state and in complex with complement C3b protein have allowed us to create a map of reactive solvent‐exposed residues on the surface of FH and to observe the changes in oxidation of FH residues upon C3b binding. Studies of the solvent accessibility of the S3 oleosin show that X‐ray footprinting offers also a unique approach to studying the structure of proteins embedded within membranes or lipid bodies. All the biomolecular applications reported herein demonstrate that the Metrology beamline at SOLEIL can be successfully used for synchrotron X‐ray footprinting of biomolecules.     

Time–space transformation of femtosecond free‐electron laser pulses by periodical multilayers

A scattering scheme to probe the time evolution of femtosecond pulses of a soft X‐ray free‐electron laser (FEL) in a multilayer structure is presented. The response of periodic multilayers (MLs) with low and high absorption and various numbers of bi‐layers to a pulse train of Gaussian‐shaped sub‐pulses is calculated. During the passage of the incident pulse the interaction length increases and the scattering profile changes as a function of the spatial position of the pulse within the sample. Owing to stretching of the reflected pulse compared with the incident pulse, the time‐dependent scattering evolution in the ML can be visualized along a spatial coordinate of a position‐sensitive detector. Using a scattering geometry where the mean energy of the incident pulse train is slightly detuned from the energy of maximum reflectivity at the first‐order peak, the response of the ML shows an oscillator behaviour along this spatial coordinate at the detector. For a FEL wavelength of 6.4 nm this effect is promising for MLs with low absorption, such as La/C for example. On the other hand, the oscillations will not be present for MLs with high absorption. Therefore a low‐absorbing ML is a sensitive tool for studying the possible change of sample absorption caused by femtosecond‐pulse interaction with matter.     

A confocal set‐up for micro‐XRF and XAFS experiments using diamond‐anvil cells

A confocal set‐up is presented that improves micro‐XRF and XAFS experiments with high‐pressure diamond‐anvil cells (DACs). In this experiment a probing volume is defined by the focus of the incoming synchrotron radiation beam and that of a polycapillary X‐ray half‐lens with a very long working distance, which is placed in front of the fluorescence detector. This set‐up enhances the quality of the fluorescence and XAFS spectra, and thus the sensitivity for detecting elements at low concentrations. It efficiently suppresses signal from outside the sample chamber, which stems from elastic and inelastic scattering of the incoming beam by the diamond anvils as well as from excitation of fluorescence from the body of the DAC.     

Development of a two‐dimensional imaging system of X‐ray absorption fine structure

A two‐dimensional imaging system of X‐ray absorption fine structure (XAFS) has been developed at beamline BL‐4 of the Synchrotron Radiation Center of Ritsumeikan University. The system mainly consists of an ionization chamber for I₀ measurement, a sample stage, and a two‐dimensional complementary metal oxide semiconductor (CMOS) image sensor for measuring the transmitted X‐ray intensity. The X‐ray energy shift in the vertical direction, which originates from the vertical divergence of the X‐ray beam on the monochromator surface, is corrected by considering the geometrical configuration of the monochromator. This energy correction improves the energy resolution of the XAFS spectrum because each pixel in the CMOS detector has a very small vertical acceptance of ～0.5 µrad. A data analysis system has also been developed to automatically determine the energy of the absorption edge. This allows the chemical species to be mapped based on the XANES feature over a wide area of 4.8 mm (H) × 3.6 mm (V) with a resolution of 10 µm × 10 µm. The system has been applied to the chemical state mapping of the Mn species in a LiMn₂O₄ cathode. The heterogeneous distribution of the Mn oxidation state is demonstrated and is considered to relate to the slow delocalization of Li⁺‐defect sites in the spinel crystal structure. The two‐dimensional‐imaging XAFS system is expected to be a powerful tool for analyzing the spatial distributions of chemical species in many heterogeneous materials such as battery electrodes.     

Mini‐beam collimator enables microcrystallography experiments on standard beamlines

The high‐brilliance X‐ray beams from undulator sources at third‐generation synchrotron facilities are excellent tools for solving crystal structures of important and challenging biological macromolecules and complexes. However, many of the most important structural targets yield crystals that are too small or too inhomogeneous for a `standard' beam from an undulator source, ～25–50 µm (FWHM) in the vertical and 50–100 µm in the horizontal direction. Although many synchrotron facilities have microfocus beamlines for other applications, this capability for macromolecular crystallography was pioneered at ID‐13 of the ESRF. The National Institute of General Medical Sciences and National Cancer Institute Collaborative Access Team (GM/CA‐CAT) dual canted undulator beamlines at the APS deliver high‐intensity focused beams with a minimum focal size of 20 µm × 65 µm at the sample position. To meet growing user demand for beams to study samples of 10 µm or less, a `mini‐beam' apparatus was developed that conditions the focused beam to either 5 µm or 10 µm (FWHM) diameter with high intensity. The mini‐beam has a symmetric Gaussian shape in both the horizontal and vertical directions, and reduces the vertical divergence of the focused beam by 25%. Significant reduction in background was achieved by implementation of both forward‐ and back‐scatter guards. A unique triple‐collimator apparatus, which has been in routine use on both undulator beamlines since February 2008, allows users to rapidly interchange the focused beam and conditioned mini‐beams of two sizes with a single mouse click. The device and the beam are stable over many hours of routine operation. The rapid‐exchange capability has greatly facilitated sample screening and resulted in several structures that could not have been obtained with the larger focused beam.     

A new ultra‐high‐vacuum variable temperature and high‐magnetic‐field X‐ray magnetic circular dichroism facility at LNLS

X‐ray magnetic circular dichroism (XMCD) is one of the most powerful tools for investigating the magnetic properties of different types of materials that display ferromagnetic behavior. Compared with other magnetic‐sensitive techniques, XMCD has the advantage of being element specific and is capable of separating the spin and magnetic moment contributions associated with each element in the sample. In samples involving, for example, buried atoms, clusters on surfaces or at interfaces, ultrathin films, nanoparticles and nanostructures, three experimental conditions must be present to perform state‐of‐the‐art XMCD measurements: high magnetic fields, low temperatures and an ultra‐high‐vacuum environment. This paper describes a new apparatus that can be easily installed at different X‐ray and UV beamlines at the Brazilian Synchrotron Light Laboratory (LNLS). The apparatus combines the three characteristics described above and different methods to measure the absorption signal. It also permits in situ sample preparation and transfer to another chamber for measurement by conventional surface science techniques such as low‐energy electron diffraction (LEED), reflection high‐energy electron diffraction (RHEED), X‐ray photoelectron spectroscopy (XPS) and X‐ray photoelectron diffraction (XPD). Examples are given of XMCD measurements performed with this set‐up on different materials.     

A compact permanent‐magnet system for measuring magnetic circular dichroism in resonant inelastic soft X‐ray scattering

A compact and portable magnet system for measuring magnetic dichroism in resonant inelastic soft X‐ray scattering (SX‐RIXS) has been developed at the beamline BL07LSU in SPring‐8. A magnetic circuit composed of Nd–Fe–B permanent magnets, which realised ～0.25 T at the center of an 11 mm gap, was rotatable around the axis perpendicular to the X‐ray scattering plane. Using the system, a SX‐RIXS spectrum was obtained under the application of the magnetic field at an angle parallel, nearly 45° or perpendicular to the incident X‐rays. A dedicated sample stage was also designed to be as compact as possible, making it possible to perform SX‐RIXS measurements at arbitrary incident angles by rotating the sample stage in the gap between the magnetic poles. This system enables facile studies of magnetic dichroism in SX‐RIXS for various experimental geometries of the sample and the magnetic field. A brief demonstration of the application is presented.