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Genomic Science Program

User Facilities Enabling Science

Advanced Technologies for Biology

Synchrotron and Neutron Beam Facilities Accelerating Biological Research

Synchrotron light sources and neutron facilities at the Department of Energy's (DOE) national laboratories enable understanding of the structure of matter down to the atomic or molecular level using approaches not possible with laboratory instrumentation. Synchrotron facilities produce intense beams of photons, from X-rays to infrared to terahertz radiation, while neutron facilities produce beams using particle accelerators or reactors. The beams are directed into experimental stations housing instruments configured for specific biological investigations.

This infrastructure provides user access to beamlines and instrumentation for high-resolution studies of biological organisms and molecules for all areas of research in the life sciences. Users are chosen through a peer–reviewed proposal process managed by each facility. Capabilities of and contact information for each station are described below. To find out more about what each experimental program offers, contact the facilities directly.

This activity is supported by DOE’s Office of Biological and Environmental Research within the Office of Science and is closely coordinated with other federal agencies and private organizations.

BER's Structural Biology Experimental Stations

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    SBC User Highlights
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  • Structural Biology Center (SBC) at the Advanced Photon Source
    SBC is a major protein crystallography research facility that enables the atomic-scale study of macromolecular systems using extremely small (micron-size) crystal samples. SBC's two experimental stations—the insertion device (ID) beamline and the bending-magnet beamline—are among the most powerful and focused X-ray sources available for structural biology. Output is enhanced by on-axis sample viewing optics; easy access to minibeams (5, 10, and 20 μm) and variable beam sizes (25 to 250 μm); integration of computing and data-storage resources to accelerate data analysis and archiving; near real–time data interpretation, optimization of experimental parameters, and structure solution; and full integration of synchrotron hardware, detectors, crystal mounting robot, beamline software, and crystallographic software packages. These capabilities provide not just diffraction data, but also an interpretable electron density map and a macromolecular structure. For the 19-ID beamline, all these capabilities are available via remote access. SBC's beamlines can be used for a wide range of crystallographic experiments involving:
    • Crystals of macromolecular assemblies with very large unit cells
    • Crystals of membrane proteins
    • Multi- or single-wavelength anomalous diffraction (MAD/SAD) phasing
    • Small, weakly diffracting crystals
    • Ultra high-resolution crystallography
    • Cryo-crystallography

Location: Advanced Photon Source, Argonne National Laboratory, Argonne, IL
Website: http://www.sbc.anl.gov

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    PXRR User Highlight
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  • Macromolecular Crystallography Research Resource (PXRR) at the National Synchrotron Light Source
    PXRR provides facilities and support for macromolecular structure determination by synchrotron X-ray diffraction. Five PXRR beamlines, two of which are high-brightness undulators, enable highly efficient structure determination by every available crystallographic technique. Complementary spectroscopic methods, including optical absorption spectroscopy and Raman spectroscopy, enable simultaneous measurements of the same sample under nearly identical experimental conditions. PXRR also offers a popular mail-in crystallography program, builds new facilities, advances automation, and provides user support for a limited program in small-angle X-ray scattering on macromolecule solutions.

Location: National Synchrotron Light Source, Brookhaven National Laboratory, Brookhaven, NY
Website: http://www.px.nsls.bnl.gov

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    PCS User Highlights
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  • Protein Crystallography Station (PCS) at the Los Alamos Neutron Science Center
    PCS is a high-performance neutron beamline that forms the core of a capability for investigating the structure and dynamics of proteins, biological polymers, hydrogen bonding, drug binding, and membranes. Neutron diffraction is a powerful technique for locating hydrogen atoms (which can be hard to detect using X-rays) and thus can provide unique information about how biological macromolecules function and interact with each other and smaller molecules. PCS users have access to neutron beam time, deuteration facilities, technologies for studying protein expression and substrate synthesis with stable isotopes, a purification and crystallization laboratory, and software and support for data reduction and structure analysis. A recently acquired Rigaku HighFlux X-ray system enables users to collect X-ray data at room temperature from the same samples used for neutron diffraction. The PCS beamline exploits the pulsed nature of spallation neutrons and a helium-3 filled detector to collect time-of-flight Laue diffraction patterns. Data collection is efficient and has good signal to noise using all available neutrons [with a wavelength range of about 0.7 to 7.0 angstroms (Å)] in the pulsed white beam.

Location: Los Alamos Neutron Science Center, Los Alamos National Laboratory
Website: http://lansce.lanl.gov/lujan/instruments/PCS.shtml

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    SMB Center User Highlight
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  • Structural Molecular Biology (SMB) Center at the Stanford Synchrotron Radiation Lightsource (SSRL)
    The SMB Center provides beamline facilities and scientific support for biological studies that use macromolecular crystallography (MC), X-ray absorption spectroscopy (XAS), and small-angle X-ray scattering and diffraction (SAXS) to address and solve challenging problems in structural biology relevant to energy, environmental, and biomedical applications. The SMB Center also works with staff from SLAC's X-ray "free-electron" laser (Linac Coherent Light Source) to develop innovative new approaches for studying biomolecules, including nanocrystallography and femtosecond time-resolved X-ray spectroscopy.

    MC determines the three-dimensional (3D) structure of biological molecules at atomic resolution (<1 Å), thereby helping elucidate detailed mechanisms by which macromolecules function in living cells and organisms. The five MC stations provide high-intensity beams for multi- or single-wavelength anomalous diffraction (MAD/SAD) and monochromatic data collection, all with highly automated robotics-based, high-throughput crystal screening and data collection. All MC beamlines provide remote-access control, enabling users to perform measurements from their home labs. A microbeam undulator station with a large-area pixel array detector (PAD) enables studies of micron-sized crystals associated with the most challenging structural biology problems (e.g., large macromolecular complexes with large unit cells, small "micro" crystals, and radiation- and mechanically sensitive samples).

    XAS is used to obtain structural and electronic information on metal sites in biomolecules. The foci at the optimized XAS beamlines and instrumentation are on dilute metalloprotein XAS, microbeam imaging XAS, low-Z XAS (for studies of ligands such as sulfur and chlorine), polarized single-crystal XAS, and X-ray emission-based studies. The range of XAS equipment includes advanced solid-state array X-ray fluorescence detector systems, liquid helium cryostats, and Kirkpatrick-Baez optic micro-XAS instrumentation, as well as a range of sample environments. The SMB Center provides software for flexible data acquisition and on- and off-line data analysis.

    SAXS features a state-of-the-art beamline and experimental facilities for solution scattering, lipid membrane diffraction, fiber diffraction, and single-crystal diffraction at scattering angles ranging from microns to a few angstroms. These techniques, enabling structural studies of biological macromolecules and assemblies in physiological or near-physiological conditions, complement high-resolution MC structural techniques. Besides providing automated, high-throughput experimental facilities for equilibrium solution studies, the SAXS beamline maintains premier experimental facilities for time-resolved studies on time scales of milliseconds and longer.

Location: Stanford Synchrotron Radiation Lightsource at the SLAC National Accelerator Laboratory, Stanford, CA
Website: http://www-ssrl.slac.stanford.edu/

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    SIBYLS User Highlight
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  • Structurally Integrated Biology for the Life Sciences (SIBYLS) Beamline at the Advanced Light Source
    The SIBYLS beamline is a dual endstation synchrotron beamline combining macromolecular crystallography (MX) with small-angle X-ray scattering (SAXS). MX produces high-resolution structural information from biological molecules, and the high-throughput SAXS pipeline enables the same biological systems to be imaged in aqueous solution, closer to their natural state. Combining SAXS results with atomic-resolution structures provides detailed characterizations of mass, radius, conformation, assembly, and shape changes associated with protein folding and functions. SAXS also can resolve ambiguities of crystallography by showing the most likely possible structures.

Location: Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA
Website: http://sibyls.als.lbl.gov/; See also http://alsusweb.lbl.gov

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    CSMB User Highlights
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  • Center for Structural Molecular Biology (CSMB) at the High Flux Isotope Reactor and Spallation Neutron Source
    CSMB is dedicated to developing instrumentation and methods for determining the structure, function, and dynamics of complex biological systems. CSMB's suite of tools includes a small-angle neutron scattering (SANS) facility for studying biological samples under physiological (or physiologically relevant) and industrial processing conditions, small- and wide-angle X-ray scattering instruments, a bio-deuteration laboratory for in vivo isotopic labeling, and advanced computational resources for modeling proteins and protein complexes. Deuterium-labeling techniques enable scientists to selectively highlight and map chemically distinct components of larger protein-protein, protein-lipid, or protein–nucleic acid complexes and, moreover, to follow their conformational changes and assembly or disassembly processes in solution on biologically relevant time scales. These capabilities are helping researchers understand how macromolecular systems are formed and interact with other systems in living cells—ultimately bridging the information gap between cellular function and the molecular mechanisms that drive it.

Location: Oak Ridge National Laboratory, Oak Ridge, TN
Website: http://www.csmb.ornl.gov

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    ABEX User Highlight
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  • Advanced Biological and Environmental X-Ray Spectroscopy (ABEX) at the Advanced Light Source
    ABEX is a user resource at the Advanced Light Source (ALS) that enables X-ray spectroscopic characterization of complex biological and environmental systems using soft X-ray absorption spectroscopy (XAS) and X-ray magnetic circular dichroism (XMCD). These spectroscopies exploit the availability of high brightness, circularly polarized soft X-rays at ALS and offer unique advantages in analyzing the detailed electronic and magnetic structure of biological metal sites. ABEX research also develops spectroscopies, such as nuclear resonance vibrational spectroscopy (NRVS), that require high-energy storage rings.

    An ABEX instrument development program improves both the sensitivity and ease of use of its endstations for biological and environmental samples. A spectroscopy support laboratory on the ALS mezzanine provides access to electron paramagnetic resonance (EPR), infrared (IR), and resonance Raman instruments, enabling essential control measurements on samples studied by X-ray techniques.

Location: Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA
Website: http://abex.lbl.gov

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    BSISB User Highlights
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  • Berkeley Synchrotron Infrared Structural Biology (BSISB) Program at the Advanced Light Source
    BSISB provides facilities and training support for characterizing cellular chemistry and function by synchrotron radiation–based Fourier transform infrared (SR-FTIR) spectromicroscopy. Other complementary microscopy and spectroscopic imaging methods include fluorescence microscopy and simultaneous optical hyperspectral sample imaging. Aqueous environments hinder SR-FTIR's sensitivity to bacterial activity, but BSISB's integrated in situ open-channel microfluidic culturing systems circumvent the water-absorption barrier while allowing cells to maintain their functions. These technological systems enable real-time chemical imaging of bacterial activities in biofilms and facilitate comprehensive understanding of structural and functional dynamics in a wide range of microbial systems. BSISB continues to build new chemical imaging capabilities, advance user-specific microfluidic systems and automation, and develop new software for accelerating data analysis.

Location: Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA
Website: infrared.als.lbl.gov

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    NCXT User Highlight
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  • National Center for X-Ray Tomography (NCXT) at the Advanced Light Source
    NCXT is leading the development of soft X-ray tomography (SXT) as a technique for imaging fully hydrated biological specimens at high, three-dimensional (3D) spatial resolution. SXT has several distinct advantages over light- and electron-based microscopies and, as a result, can contribute unique insights on cell structure and behavior. Soft X-rays penetrate biological materials much more deeply than electrons, allowing cells up to 15 μm thick to be imaged intact. SXT image contrast is generated by differential X-ray absorption by biomolecules, meaning that cells advantageously do not require exposure to staining or other potentially damaging procedures prior to being imaged. Consequently, SXT produces high-resolution specimen views that are in a close-to-native state.

    SXT's utility has been increased dramatically by the concomitant development of high-aperture cryogenic fluorescence tomography (CFT). Cryo-preserved cells, or populations of cells, can now be imaged serially by two disparate tomographic methods. The combination of CFT and SXT allows labeled molecules to be positioned accurately and viewed directly in the context of a high-resolution, quantitative 3D tomographic cell reconstruction.

Location: Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA
Website: http://ncxt.lbl.gov

For more information about DOE structural biology resources, contact:

Amy Swain
Biological Systems Science Division
U.S. Department of Energy Office of Science
301-903-1828
Email format for contacting Swain: firstname.lastname@science.doe.gov

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Advanced Technologies for Biology brochure


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DOE JGI Strategic Planning for the Genomic Sciences [8/12]


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Applications of New DOE National User Facilities in Biology report


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