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Biomedical Technology Resources Directory

Synchrotron Radiation

 
BioCARS: A Synchrotron Structural Biology Resource
Biophysics Collaborative Access Team (BioCAT)
Macromolecular Crystallography at the National Synchrotron Light Source
Macromolecular Diffraction Biotechnology Resource
Synchrotron Radiation Structural Biology Resource
Undulator Resource for Structural Biology

 
BioCARS: A Synchrotron Structural Biology Resource
University of Chicago
5640 South Ellis
Chicago, IL 60637
http://cars.uchicago.edu/

Grant No. P41 RR007707
Principal Investigator and Contact
Keith Moffat, Ph.D.
773-702-2116; Fax: 773-702-0439
E-mail: moffat@cars.uchicago.edu

Research Emphasis

BioCARS梐 component of the Consortium for Advanced Radiation Sources (CARS)梚s operating Sector 14 at the Advanced Photon Source at Argonne National Laboratory as a national user facility for synchrotron radiation research. The scientific interests of BioCARS are crystallographic studies of viruses, ribosomes, and other complexes with very large unit cells; studies of microcrystals; time-resolved crystallography; and scattering from less-ordered biological systems. In all cases, the goal is to understand basic biological processes in structural terms, a goal fundamental to the pharmaceutical and biotechnology industries as well as to basic science.

Current Research

Design and construction of novel optical elements to deliver the brilliant X-ray beam to the crystals; design and construction of all components necessary to equip one sector at the Advanced Photon Source consisting of one insertion device and one bending magnet beamline; novel forms of X-ray detectors; and strategies for the effective acquisition of precise MAD data and time-resolved data.

Resource Capabilities

Instruments

Appropriate hardware and software for experiments in the areas outlined. BioCARS also is equipped with a Biosafety Level 3 facility for operation of all stations and control areas in BSL2 or BSL3 modes.

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Biophysics Collaborative Access Team (BioCAT)
Illinois Institute of Technology
BCPS/CSRRI
3101 South Dearborn Street
Chicago, IL 60616
www.bio.aps.anl.gov/

Grant No. P41 RR008630
Principal Investigator and Contact
Thomas Irving, Ph.D.
312-567-3489; Fax: 312-567-3494
E-mail: irving@biocat1.iit.edu

Alternate Contacts
Clareen Krolik
630-252-0549; Fax: 630-252-0545
E-mail: krolik@bio.aps.anl.gov

Research Emphasis

BioCAT has constructed and now operates facilities at Argonne National Laboratory抯 Advanced Photon Source (APS) as a national research resource for the study of the structure of partially ordered biological molecules, complexes of biomolecules, and cellular structures under conditions similar to those present in living cells and tissues. The goal of BioCAT抯 research is to determine the detailed structure and mechanism of action of biological systems at the molecular level. The techniques employed are X-ray fiber diffraction; X-ray solution scattering; and X-ray absorption spectroscopy, with an emphasis on time-resolved and space-resolved studies and development of novel techniques.

Current Research

Typical applications: X-ray diffraction of biological fibers such as muscle and collagen; membrane/protein systems; solution scattering of proteins and nucleic acids; time-resolved protein folding. XAFS studies of metalloproteins and their complexes; site-selective XAFS by high-resolution emission spectroscopy; X-ray Raman spectroscopy; in situ spectroscopy and X-ray scattering in tissues as they relate to disease processes. Instrumentation development. Novel detector designs. Improved data acquisition, data evaluation, and robust data analysis methods.

Resource Capabilities

Facilities

APS undulator A beamline, fixed exit height, cryogenically cooled silicon monochromators, energy range 3.5� KeV Si(111), 8� KeV Si(400) using the first harmonic, up to 70 KeV with the second harmonic of Si(400); one-meter-long harmonic rejection/vertical focusing mirror, crystal horizontal sagittal focusing. Rapid crystal change with dual monochromators. Quick scanning capability: QXAFS scans in seconds. Measured flux at 7 KeV is ~5 times 1013 photons/sec into a focal spot that is vertically adjustable between <20 祄 to ~1 mm vertical, and horizontally adjustable from <200 祄 to ~4 mm with full beam flux. Independent horizontal and vertical focus. Smaller beams (micron scale) are available at reduced flux. 0.3� small-angle X-ray scattering (SAXS) camera. Ionization chambers, large acceptance multilayer analyzer/detector for fluorescence XAFS and microprobe, CCD, image plate, and high-rate linear multi-element detector for SAXS. Software for time-resolved data acquisition; shortest time slicing interval in standard setup for XAFS and MED ~1 m. Apparatus for optical monitoring of sample integrity; polarized XAFS goniometer; stopped flow system; low vibration closed-cycle helium refrigerator for sample cooling. Sample preparation and characterization laboratory adjacent to beamline; electronics laboratory. Workstation with data analysis software for XAFS and SAS. Periodic training workshops.

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Macromolecular Crystallography at the National Synchrotron Light Source
Brookhaven National Laboratory
Department of Biology
Upton, NY 11973
www.px.nsls.bnl.gov/

Grant No. P41 RR012408
Principal Investigator
Robert M. Sweet, Ph.D.
631-344-3401; Fax: 631-344-3407
E-mail: sweet@bnl.gov

Contact
For current contact information, please check the resource web site.

Research Emphasis

The focus of this resource is to advance the state of macromolecular crystallography (PX) at the National Synchrotron Light Source (NSLS), with dissemination of research methods, designs, and computer codes to other synchrotron sources around the world. The resource teaches a world-class course in rapid synchrotron data collection for PX and structure solving. A summary of the resource programs can be found at www.px.nsls.bnl.gov/rr_summary/brief_intro/brief_intro.html.

Current Research

There are five major research projects under way in the resource (www.x12c.nsls.bnl.gov/rr_summary/rr_summary.html): Development of the wiggler beamline X25 for macromolecular crystallography; development of a shared computing system from inexpensive commodity computers; remote monitoring and operation of beamline processes; use of multilayer monochromators for macromolecular crystallography; and three-beam phasing for macromolecular crystallography (www.px.nsls.bnl.gov/3bd/).

Resource Capabilities

Five NSLS beamlines are tied together in a consortium dedicated to PX. Two constructed with Department of Energy funding in the early 1980s, X12-B and X12-C, support a wide range of outside users, who gain access through the peer-reviewed General User Program of the NSLS, collaborators of the NCRR resource, and users from within the Biology Department抯 research program. At least half of the beam time at the wiggler beamline X25 is devoted to PX. Similarly, in collaboration with the biophysics group at Los Alamos National Laboratory, X8-C was built up, and Cold Spring Harbor Laboratory, SUNY Stony Brook, and Georgia Research Alliance joined the Biology Department of the Brookhaven National Laboratory to bring X26C online; 25% of these two beamlines� time is available to general users. All beamlines are equipped with CCD-based area detectors, and three have four-circle diffractometers bearing the detectors. MAD phasing is performed routinely, and study of very high resolution diffraction or very large unit cells is available.

  1. Murakami, K., Masuda, S., and Darst, S., Structural basis of transcription initiation: T. aquaticus RNA polymerase holoenzyme at 4 � resolution. Science 296:1280�84, 2002.
  2. Zhou, Y., Morais-Cabral, J., et al., Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 � resolution. Nature 414:43�, 2001.
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Macromolecular Diffraction Biotechnology Resource
Cornell University
Wilson Synchrotron Lab
Ithaca, NY 14853-8001
www.macchess.cornell.edu/

Grant No. P41 RR001646
Principal Investigator
Sol M. Gruner, Ph.D.
607-255-3441; Fax: 607-255-8751
E-mail: smg26@cornell.edu

Contact
Quan Hao, Ph.D.
607-254-8983; Fax: 607-255-9001
E-mail: qh22@cornell.edu

Research Emphasis

This resource, also known as MacCHESS, operates three insertion-device beamlines (stations A-1, F-1, and F-2) at the Cornell High Energy Synchrotron Source (CHESS) devoted to macromolecular crystallography. In addition, the resource supports additional bending magnet stations for part-time macromolecular X-ray experiments. The resource specializes in large unit-cell diffraction, ultra-high resolution diffraction, MAD phasing, rapid-throughput crystallography (structure-based drug design and structural genomics), microdiffraction, multiple-beam diffraction, and software development.

Resource Capabilities

Unit cells as large as 1400 � have been resolved. Diffraction to 0.72 � has been collected. Structures as large as 370 KDa have been solved by MAD phasing. As many as 70 selenium atoms have been located from anomalous data. Datasets from ideal crystals can be collected in a few seconds. Typical exposure times vary from 5 to 120 seconds. The resource is sufficiently efficient to accommodate hundreds of researchers each year.

Instruments

All stations utilize CCD area detectors. Image plates are also available. Sample cryo coolers are available at the three wiggler stations. Station A-1 is for monochromatic measurements; a 49-pole wiggler replaces the 24-pole wiggler. Station F-1 is a monochromatic X-ray station designed to accommodate large unit-cell samples. The station is equipped with a biohazard containment facility rated at the Biosafety Level 3. Station F-2 is a tunable facility designed for MAD phasing from which the X-ray energy can be tuned from 7.9 to 16 KeV. A cold room is present on site; microscopes are available at all stations. 3-D graphics are available on some computers. Over a dozen Alpha computers support data processing.

Software

A data collection GUI provides ease in collecting the diffraction data. All station hardware motors are controlled with simple software. X-ray diffraction data are analyzed using the DPS/Mosflm and DENZO software.

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Synchrotron Radiation Structural Biology Resource
Stanford University
Stanford Synchrotron Radiation Laboratory
Department of Chemistry
Stanford, CA 94305
http://smb.slac.stanford.edu/

Grant No. P41 RR001209
Principal Investigator
Keith O. Hodgson, Ph.D.
650-926-3153; Fax: 650-926-4100
E-mail: hodgson@ssrl.slac.stanford.edu

Contact
Lisa Dunn
650-926-2087
E-mail: lisa@ssrl.slac.stanford.edu

Research Emphasis

Stanford Synchrotron Radiation Laboratory (SSRL) provides synchrotron radiation for research in several fields, including structural molecular biology, for which about 9 stations are dedicated 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 R&D 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/data reduction stations are available for high-throughput, high-resolution, MAD-phasing and monochromatic crystallography studies. XAS capabilities include high-resolution multi-element detectors and low-temperature cryostats for dilute protein solution studies on stations covering the energy range 2� 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

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 5.9–20 keV (0.62–2.1 �) and is equipped with a Quantum 315 detector system. Bending magnet BL1-5 has an energy range of 5.9–16 keV and is equipped with a Quantum 4 detector. Wiggler side-stations BL11-1 and BL9-1 are tunable and have sufficient energy resolution for many MAD/SAD experiments. BL11-1 is a PRT beamline with 33% general user access and is equipped with a Quantum 315 detector. BL9-1 has an energy range of 12.5� keV (0.73�99 �) and is equipped with a Quantum 4 detector, and will soon be upgraded to a Quantum 315. The wiggler side-station BL7-1 operates at a fixed energy of 11.5 keV (1.08 �) and is equipped with a MAR-345 detector. Experiments are carried out using the BLU-ICE interface. All beamlines (except 7-1) 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: A multipurpose SAXS camera is available for use on a semi-dedicated wiggler end-station (~75% of total beam time currently). A stopped-flow rapid mixer and a continuous-flow jet mixer are available for time-resolved SAXS studies of proteins in solution. A very-low-angle single crystal diffraction system (10�0 �) is available for macromolecular crystallography. Detectors include linear and quadrant wire detectors and CCD detectors. Dedicated computer facilities, data acquisition and analysis software are provided.

X-ray absorption spectroscopy: Two dedicated wiggler and five shared wiggler or bending magnet stations are available, equipped with high-throughput/high-energy resolution 30- and 13-element Ge array detectors or ionization chamber detectors for fluorescence measurements of biological samples in the sub-millimolar to millimolar concentration range. Four liquid He cryostats are available for data collection at temperatures as low as 4 K. Interactive software on dedicated computers allows users to measure and analyze AS data and display results online. Micro-imaging and single-crystal XAS instrumentation is under development.

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Undulator Resource for Structural Biology
Baker Laboratory
Department of Chemistry and Chemical Biology
Cornell University
Ithaca, NY 14853-1301
http://necat.chem.cornell.edu

Grant No. P41 RR015301
Principal Investigator
Steven E. Ealick, Ph.D.
607-255-7961; Fax: 607-255-1227
E-mail: see3@cornell.edu

Contact
Leslie Kinsland
607-255-1112; Fax: 607-255-1227
E-mail: lk65@cornell.edu

Research Emphasis

The Undulator Resource for Structural Biology is a planned facility for macromolecular crystallography at Sectors 8 and 24 of the Advanced Photon Source at Argonne National Laboratory. The resource is overseen by the Northeastern Collaborative Access Team (NE-CAT), which includes scientists from Columbia University, Cornell University, Harvard University, the Massachusetts Institute of Technology, Memorial Sloan Kettering Cancer Center, Rockefeller University, and Yale University. Research emphasis is placed on signal transduction, DNA transcription initiation and regulation, cell cycle regulation, virus structure and function, membrane proteins, protein folding, and enzyme structure and function. Many of the research projects focus on how biological molecules interact to form large macromolecular complexes. The macromolecules studied by NE-CAT often involve large unit cells, small crystals, weakly diffracting crystals, and crystals with weak anomalous scattering. Construction of the undulator resource requires development of a novel dual undulator design utilizing components developed by the Advanced Photon Source. Other technological research will focus on diamond monochromators, focusing optics, methods of phase determination, radiation damage, X-ray detectors, and crystallographic software.

The Undulator Resource for Structural Biology will provide advanced synchrotron beamlines for macromolecular crystallography. The resource also provides laboratory space for protein production and crystallization and office space for data analysis. Upon completion, the undulator resource will provide three high-brilliance undulator beamlines and one bending magnet beamline. Each beamline will be equipped with X-ray detectors, cryocoolers, and other instrumentation for X-ray diffraction.

8-BM (end-station): Currently in commissioning phase. Features include a precollimator mirror, vertical offset, sagittally focusing monochromator (5� KeV, 2 eV bandpass), ADSC Quantum 315 detector, Huber 515 Kappa goniometer, Oxford Cryojet.

24-ID (end-station): Planned for late 2003. Features include a vertical offset diamond monochromator (5� KeV, 2 eV bandpass), Kirkpatrick朆aez focusing, target flux (1013 ph/s in 100 times 100 mm2 at 12 KeV).

24-ID (side-station): Planned for late 2004. Features include a horizontal offset diamond transmission monochromator (9� KeV, 2 eV bandpass), Kirkpatrick朆aez focusing, target flux (1012 ph/s in 100 times 100 mm2 at 12 KeV).

24-ID (fixed-wavelength side-station): Planned for late 2005. Features include a single-bounce diamond monochromator (fixed 12 KeV, 2 eV bandpass), Kirkpatrick朆aez focusing, target flux (1012 ph/s in 100 times 100 mm2 at 12 KeV).

Other facilities: 8,000 square feet of laboratory and office space in LOM436, including biochemical and computing facilities.

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