08B1‐1: an automated beamline for macromolecular crystallography experiments at the Canadian Light Source

Beamline 08B1‐1 is a recently commissioned bending‐magnet beamline at the Canadian Light Source. The beamline is designed for automation and remote access. Together with the undulator‐based beamline 08ID‐1, they constitute the Canadian Macromolecular Crystallography Facility. This paper describes the design, specifications, hardware and software of beamline 08B1‐1. A few scientific results using data obtained at the beamline will be highlighted.     

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.     

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.     

MxDC and MxLIVE: software for data acquisition,information management and remote access to macromolecular crystallography beamlines

An integrated computer software system for on‐site and remote collection of macromolecular crystallography (MX) data at the Canadian Light Source (CLS) is described. The system consists of an integrated graphical user interface for data collection and beamline control [MX Data Collector (MxDC)] which provides experiment‐focused control of beamline devices, and a laboratory information management system [MX Laboratory Information Virtual Environment (MxLIVE)] for managing sample and experiment information through a web browser. The system allows remote planning and transmission of sample and experiment parameters to the beamline through MxLIVE, on‐site or remote data collection through MxDC guided by information from MxLIVE, and remote monitoring and download of experimental results through MxLIVE. The system is deployed and in use on both MX beamlines at the CLS which constitute the Canadian Macromolecular Crystallography Facility.     

ID29: a high‐intensity highly automated ESRF beamline for macromolecular crystallography experiments exploiting anomalous scattering

ID29 is an ESRF undulator beamline with a routinely accessible energy range of between 20.0 keV and 6.0 keV (λ = 0.62 Å to 2.07 Å) dedicated to the use of anomalous dispersion techniques in macromolecular crystallography. Since the beamline was first commissioned in 2001, ID29 has, in order to provide an improved service to both its academic and proprietary users, been the subject of almost continuous upgrade and refurbishment. It is now also the home to the ESRF Cryobench facility, ID29S. Here, the current status of the beamline is described and plans for its future are briefly outlined.     

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.     

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.     

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.     

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.     

Forty years of metrology with synchrotron radiation at SURF

The Canadian Light Source, the University of Western Ontario, IBM Canada and BigBangwidth during 2006 developed the Remote Beamline Access (RBA) system. This system was demonstrated using a standalone soft X-ray machine as well on the VESPERS beamline. The RBA system serves as a proof of concept and basis for ScienceStudio, which is now under development.     

Performance on absolute scattering intensity calibration and protein molecular weight determination at BL16B1, a dedicated SAXS beamline at SSRF

The optical system and end‐station of bending‐magnet beamline BL16B1, dedicated to small‐angle X‐ray scattering (SAXS) at the Shanghai Synchrotron Radiation Facility, is described. Constructed in 2009 and upgraded in 2013, this beamline has been open to users since May 2009 and supports methodologies including SAXS, wide‐angle X‐ray scattering (WAXS), simultaneous SAXS/WAXS, grazing‐incidence small‐angle X‐ray scattering (GISAXS) and anomalous small‐angle X‐ray scattering (ASAXS). Considering that an increasing necessity for absolute calibration of SAXS intensity has been recognized in in‐depth investigations, SAXS intensity is re‐stated according to the extent of data processing, and the absolute intensity is suggested to be a unified presentation of SAXS data in this article. Theory with a practical procedure for absolute intensity calibration is established based on BL16B1, using glass carbon and water as primary and secondary standards, respectively. The calibration procedure can be completed in minutes and shows good reliability under different conditions. An empirical line of scale factor estimation is also established for any specific SAXS setup at the beamline. Beamline performance on molecular weight (MW) determination is provided as a straightforward application and verification of the absolute intensity calibration. Results show good accuracy with a deviation of less than 10% compared with the known value, which is also the best attainable accuracy in recent studies using SAXS to measure protein MW. Fast MW measurement following the demonstrated method also enables an instant check or pre‐diagnosis of the SAXS performance to improve the data acquisition.     

Are you centered? An automatic crystal‐centering method for high‐throughput macromolecular crystallography

Crystal centering is a key step in macromolecular X‐ray crystallography experiments. A new method using image‐processing and machine‐vision techniques allows the centering of small crystals in the X‐ray beam. This method positions crystals even when the loop is initially out of the camera's field of view and adapts to the difficulty of the experiment. The process has been tested on many diverse crystals with a 93% success rate when compared with manual centering.     

Focusing,collimation and flux throughput at the IMCA‐CAT bending‐magnet beamline at the Advanced Photon Source

The IMCA‐CAT bending‐magnet beamline was upgraded with a collimating mirror in order to achieve the energy resolution required to conduct high‐quality multi‐ and single‐wavelength anomalous diffraction (MAD/SAD) experiments without sacrificing beamline flux throughput. Following the upgrade, the bending‐magnet beamline achieves a flux of 8 × 10¹¹ photons s^?1 at 1 Å wavelength, at a beamline aperture of 1.5 mrad (horizontal) × 86 µrad (vertical), with energy resolution (limited mostly by the intrinsic resolution of the monochromator optics) δE/E = 1.5 × 10^?4 (at 10 kV). The beamline operates in a dynamic range of 7.5–17.5 keV and delivers to the sample focused beam of size (FWHM) 240 µm (horizontally) × 160 µm (vertically). The performance of the 17‐BM beamline optics and its deviation from ideally shaped optics is evaluated in the context of the requirements imposed by the needs of protein crystallography experiments. An assessment of flux losses is given in relation to the (geometric) properties of major beamline components.     

A combined microRaman and microdiffraction set‐up at the European Synchrotron Radiation Facility ID13 beamline

This article describes the current status of the microRaman set‐up at the ID13 beamline of the European Synchrotron Radiation Facility. This offers an in situ on‐axis microprobe which has a common focal position to the X‐ray microbeam and can collect spectral data simultaneously. It can also be used in an offline sample characterization role, both before and after beamline experiments. To demonstrate the application of microRaman spectroscopy within a beamline environment, a number of examples are given.     

WIFIP: a web‐based user interface for automated synchrotron beamlines

The beamline control software, through the associated graphical user interface (GUI), is the user access point to the experiment, interacting with synchrotron beamline components and providing automated routines. FIP, the French beamline for the Investigation of Proteins, is a highly automatized macromolecular crystallography (MX) beamline at the European Synchrotron Radiation Facility. On such a beamline, a significant number of users choose to control their experiment remotely. This is often performed with a limited bandwidth and from a large choice of computers and operating systems. Furthermore, this has to be possible in a rapidly evolving experimental environment, where new developments have to be easily integrated. To face these challenges, a light, platform‐independent, control software and associated GUI are required. Here, WIFIP, a web‐based user interface developed at FIP, is described. Further than being the present FIP control interface, WIFIP is also a proof of concept for future MX control software.     

Image guidance protocol for synchrotron microbeam radiation therapy

The protocol for image‐guided microbeam radiotherapy (MRT) developed for the Australian Synchrotron's Imaging and Medical Beamline (IMBL) is described. The protocol has been designed for the small‐animal MRT station of IMBL to enable future preclinical trials on rodents. The image guidance procedure allows for low‐dose monochromatic imaging at 50 keV and subsequent semi‐automated sample alignment in 3D with sub‐100 µm accuracy. Following the alignment, a beamline operation mode change is performed and the relevant beamline components are automatically aligned for the treatment (pink) beam to be delivered on the sample. Here, the small‐animal MRT station, the parameters and procedures for the image guidance protocol, as well as the experimental imaging results using phantoms are described. Furthermore, the experimental validation of the protocol using 3D PRESAGE^® dosimeters is reported. It is demonstrated that the sample alignment is maintained after the mode change and the treatment can be delivered within the same spatial accuracy of 100 µm. The results indicate that the proposed approach is viable for preclinical trials of small‐animal MRT.     

Characterization of wax as a potential diffraction intensity standard for macromolecular crystallography beamlines

A number of commercially available waxes in the form of thin disc samples have been investigated as possible diffraction intensity standards for macromolecular crystallography synchrotron beamlines. Synchrotron X‐ray powder diffraction measurements show that beeswax offers the best performance of these waxes owing to its polycrystallinity. Crystallographic lattice parameters and diffraction intensities were examined between 281 and 309 K, and show stable and predictable thermal behaviour. Using an X‐ray beam of known incident flux at λ = 1 Å, the diffraction power of two strong Bragg reflections for beeswax were quantified as a function of sample thickness and normalized to 10¹⁰ photons s^?1. To demonstrate its feasibility as a diffraction intensity standard, test measurements were then performed on a new third‐generation macromolecular crystallography synchrotron beamline.     

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.     

Design and performance of an ultra‐high‐vacuum‐compatible artificial channel‐cut monochromator

The design and performance of a novel ultra‐high‐vacuum‐compatible artificial channel‐cut monochromator that has been commissioned at undulator beamline 8‐ID‐I at the Advanced Photon Source are presented. Details of the mechanical and optical design, control system implementation and performance of the new device are given. The monochromator was designed to meet the challenging stability and optical requirements of the X‐ray photon correlation spectroscopy program hosted at this beamline. In particular, the device incorporates a novel in‐vacuum sine‐bar drive mechanism for the combined pitch motion of the two crystals and a flexure‐based high‐stiffness weak‐link mechanism for fine‐tuning the pitch and roll of the second crystal relative to the first crystal. The monochromator delivers an exceptionally uniform and stable beam and thereby improved brilliance preservation.