Synchrotron Radiation Structural Biology Resource

Synchrotron Radiation Structural Biology Resource

Research Emphasis

Current Research

Stanford Synchrotron Radiation Laboratory (SSRL) provides synchrotron radiation for research in several fields, including structural molecular biology (SMB), for which about 9 stations are dedicated to SMB with access through a peer-reviewed proposal mechanism. The NCRR resource, which operates in synergy with programs funded by the Department of Energy, Office of Biological and Environmental Research, and the National Institute of General Medical Sciences, explicitly provides research and development and dedicated user support teams for research in macromolecular crystallography, X-ray absorption spectroscopy (XAS), and small-angle X-ray scattering (SAXS).

State-of-the-art macromolecular crystallography data collection and data reduction stations are available for high-throughput, high-resolution, MAD-phasing and monochromatic crystallography studies. XAS capabilities include high-resolution multielement detectors and low-temperature cryostats for dilute protein solution, polarized single crystal, and XAS imaging studies on stations covering the energy range 2-35 keV. For SAXS, instrumentation for both static and rapid mixing time-resolved solution scattering studies is provided. A low-angle single-crystal diffraction system is also available.

Resource Capabilities

Methods

Macromolecular crystallography, X-ray absorption spectroscopy, and small-angle X-ray scattering.

Instruments

Macromolecular crystallography: End-stations BL9-2 and BL1-5 are fully tunable with excellent energy resolution for performing MAD experiments. Wiggler end-station BL9-2 has an energy range of 6 - 15 keV (0.83 - 2.06 Å) and is equipped with a MAR-325 charge-coupled device (CCD0 detector system. Bending magnet BL1-5 has an energy range of 6 - 14.5 keV (0.85 - 2.06 Å) and is equipped with a Quantum-315 detector. Wiggler side-stations BL11-1 and BL9-1 are tunable and have sufficient energy resolution for many MAD/single-wavelength anomalous dispersion (SAD) experiments, particularly at the Se edge. BL11-1 is a PRT beamline with 33% general user access and is equipped with a Quantum-315 CCD detector. BL9-1 has an energy range of 12.5 - 16 keV (0.77 - 0.98 Å) and is equipped with a Quantum-315 CCD detector. The wiggler side-station BL7-1 has recently been upgraded to operate with an energy range of 7 -13.5 keV (1.1 - 1.7 Å), and will be equipped with a Quantum-315 CCD detector. Wiggler side-station BL11-3 is a fixed energy source at 12.7 keV (0.97 Å) which is equally shared between crystallography partners and material science groups. Experiments are carried out using the Blu-Ice interface. All beam lines have automated screening systems that support three 96-pin cassettes. Collaborative tools are available for remote data collection and processing. Variable cryostats, cryotools, Xe/Kr derivatizers, microscopes, incubators, dewars, cold rooms, and stereo visualization equipment are also provided.

Small-angle X-ray scattering: Wiggler end-station BL4-2 is dedicated to scattering and diffraction studies on (mostly) non-crystalline biological systems. Highly developed data collection facilities, including advanced sample handling devices, such as stopped-flow and flow-cells, are provided for solution, lipid, and fiber studies. A double crystal monochromator allows for anomalous scattering studies, and a high-flux multilayer monochromator is available for fast time-resolved studies. A MarCCD165 is used primarily for static measurements, whereas an image-intensified CCD detector system provides the ability to record time-resolved data continuously at high frame rates up to 190 Hz. A single crystal diffraction facility has been developed specifically to cover the very low resolution range (5-700 Å). Most experiments are conducted using the Blu-Ice interface with SAXS specific features. Real-time data processing software has been developed and is available at the beam line. A data file storage facility is provided.

X-ray absorption spectroscopy: Two dedicated wiggler (BLs9-3 and 7-3) and three shared wiggler or bending magnet stations are available, which are equipped with high-throughput/high-energy resolution 30- and 13-element Ge array detectors for fluorescence measurements of biological samples in the submillimolar to millimolar metal concentration range. Liquid He cryostats are available for sample temperatures down to 4 K. A combined XAS/diffraction instrument for polarized single crystal XAS, and a capillary optic-based XAS imaging setup are available on BL9-3. Interactive software for data acquisition and analysis tools for real-time data evaluation is provided.

Software

Crystallography: A unified computational environment has been developed for macromolecular crystallography experiments to handle high-speed, large-area detectors and to present a simple user environment for carrying out complex crystallography experiments. The Blu-Ice interface design is straightforward and simple to use with a tab-based layout. Blu-Ice is now available on macromolecular crystallography beam lines at other synchrotron sources.

All commonly used crystallographic data reduction, phasing, modeling, and refinement software is also supported (CCP4, Phases, Solve, CNS, XtalView, X-PLOR, Chain, O, Pymol, and Molscript). Data can be routinely indexed, integrated, and scaled in real time, and difference or anomalous Patterson maps can be calculated. Structures can be solved during a user's run by molecular replacement, single and multiple isomorphous replacement, or MAD methods. Difference maps can be calculated for crystals soaked with substrate analogs, and structures refined against newly collected data.

Small-angle X-ray scattering: Blu-Ice with SAXS-specific features for data collection, real-time data processing software, and analysis software.

X-ray absorption spectroscopy: Image correlation spectroscopy for instrument control, Ge30/Ge13 for detector control and optimization, XAS-Collect for data acquisition, and EXAFSPAK with FEFF for data analysis.

Special Features

Macromolecular crystallography users have the option to conduct diffraction experiments from their home institutions and other remote locations by means of advanced software tools that enable remote-access control of the beam lines. Remote experimenters have access to the same tools as local users and have the capability to mount, center, and screen crystalline samples and to collect, analyze, and backup diffraction data. Automated sample mounting is accomplished with the Stanford Auto-Mounting System. Beam line and experimental control is carried out using Blu-Ice/Distributed Control System (DCS), and additional remote monitoring of the experiment and data backup is supported with several Web-based applications. The highly graphic applications and computational resources at SSRL are accessed through a client/server application that uses minimal resources on the client side and has a typical response close to that obtained at the beam line. This remote capability is now available on all macromolecular crystallography beamlines and currently services approximately 50% of current users.

Available Resources

Sample preparation laboratories with gloveboxes, ultracentrifuges, spectrophotometers, freezers, incubators, coldrooms, epr spectrometer, and standard equipment.

Training Opportunities and Workshops

Structural Molecular Biology Summer Schools, hands-on workshops, lecture-based workshops, and Web-based instructions. Beamline training for users including pre-experiment consultation and postexperiment assistance.

Publications

1. See SSRL Publications & Reports.