This wide-bore 750 MHz (1H) solid-state NMR instrument was acquired with funding from NIH, via grant 1S10-OD012213-01. A brief description of the instrument’s capabilities and accessories is provided below. For detailed information about the system’s capabilities and inquiries about instrument access, please contact This email address is being protected from spambots. You need JavaScript enabled to view it..

Capabilities and Accessories

·       4.7k degree actively shielded 89 mm bore magnet.

·      Bruker Avance III HD console

·      Quadruple channel configuration

·      Dual receivers

·      Dual BCU-II/chiller-based cooling system for enhanced VT operation

·      Magic-angle-spinning (MAS) NMR probes:

o   1.3mm MAS HCN probe with enhanced VT capabilities

o   1.9mm MAS HCN probe with enhanced VT capabilities

o   3.2mm MAS HCN probe with enhanced VT capabilities and an EFree coil design for biological samples.

o   3.2mm broad-band triple channel (HXY) MAS NMR probe with conventional VT capabilities; including insers/adapters for different channel configuration

 

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X-ray Crystallography

The 1500 square foot X-ray crystallography suite on the first floor of BST3 houses the main equipment and is supplemented by two environmentally controlled rooms to grow, store, and monitor crystals, at 18°C and at 4°C temperatures. One X-ray generator and two detectors are controlled from a central room to initiate data collection, while the control room also permits direct entry to and constant visualization/adjustment of experiments going on in the adjacent generator rooms. Rigaku X-ray equipment is provided for variety of experimental sample types. The high intensity, FR-E SuperBright generator and focusing optics provide a combination of existing rotating anode expertise and microfocus X-ray generation technology, yielding a flux within the same order of magnitude as a 2nd generation synchrotron bending magnet. Both ports on each generator are utilized and detectors include a Saturn 944 CCD, and a high throughput RAXIS HTC image plate. All ports are equipped with VariMax optics to provide high intensity and highly focused X-ray beams, as well as X-stream 2000 cryogenic systems. Ports supporting the CCD detectors utilize HF (high flux) optics with computerized slit control, while HR (high resolution) optics are provided on ports supporting the image plate detectors. This mix allows for high quality data collection on small and normal sized crystals, as well as on crystals with large unit cells typically containing very large proteins, viruses, or protein-protein assemblies. In-house liquid and dry nitrogen gas is supplied for all cryogenic systems, as well as helium for beam path purging.

In addition, the department is a member of a collaborative access team (SER-CAT, sector 22) at the APS (Advanced Photon Source) in Argonne, IL, to guarantee regular, 3rd generation synchrotron access to X-ray facility members when the absolute highest resolution possible is needed, only extremely small or very weakly diffracting crystals are available, or MAD/SAD phasing experiments are needed at non-standard wavelengths.

Within the main X-ray crystallography suite are located two additional labs, devoted to mounting, and computational analysis. The optical microscopy room, facilitates crystal examination/mounting/freezing and manual monitoring of crystallization set-ups. It contains multiple Olympus SZX12, SZX7, and SZ-61 microscopes, with high-end microscopes equipped with high-resolution cameras interfaced with LCD monitors and workstations for image capturing and recording. The computational room, contains multiple workstations, to facilitate rapid processing and analysis of incoming or previously collected data.

For Small-Angle X-ray Scattering studies, an Anton Paar SAXSess mc2 instrument with a sealed tube generator is also housed in the microscopy/mounting lab. This instrument includes a unit for controlling the temperature of the sample with Peltier heating/cooling, allowing for measurement at temperatures between -30°C and 120°C with a ± 0.1°C accuracy; a μ-cell and sample holder for the measurement of very small sample volumes; and a Mythen Detector for SAXSess, which unlike standard imaging plate detectors, allows for time-resolved and automated SAXS experiments.

 

Collectively, the X-ray crystallography facility and its resources provide everything needed to carry out state of the art crystallographic analysis of macromolecules. Professor William Furey serves as Co-Director of the X-ray facility, while Mr. Doowon Lee is the day-to-day facility manager dealing with maintenance, training, and user scheduling. 

Nuclear Magnetic Resonance (NMR) spectroscopy

The NMR facility of the Department of Structural Biology occupies ~10,000sq. ft. in the basement of the BST3 Tower. This is where a complement of high field spectrometers is housed.

NMR spectroscopy is a powerful technique that can provide information on molecular structure and dynamics at the atomic level. NMR was originally developed in 1945 by the physicists Bloch and Purcell to investigate nuclear properties. It soon was adopted by chemists as the prime method for analyzing and identifying the structure of molecules. Over the years, continuous advancements and a wide array of different applications have been developed.

Structural Biologists use solution NMR to determine the three-dimensional structures of large biological macromolecules, such as proteins, DNA, RNA and complexes of these molecules. In addition, solid-state NMR allows ones to probe the structure and motion of membrane proteins.

Traditionally, proton NMR based techniques that exploit the high abundance and sensitivity of the 1H isotope were used. However, given the large number of hydrogen atoms in macromolecules, 1H spectra are highly overlapped and assignment is intractable. Fortunately, molecular biology techniques allow the incorporation of 13C, 15N and 2H into biological macromolecules. The combined methodological advances of isotope labeling and multi-dimensional heteronuclear NMR techniques make it possible to determine atomic-resolution solution structures and motions of biologically important macromolecules. Solid-state NMR methods can be applied to study the structure and dynamics of very large biomolecules such as membrane proteins or polymeric assemblies as found in amyloid fibers.

A unique feature of the NMR Facility is that it houses, in one location, instrumentation for high resolution solution and solid-state NMR spectroscopy with magnets at several field strengths. There are a total of seven spectrometers dedicated to biological NMR. These include three 600 MHz spectrometers and 700 MHz, 750 MHz, 800 MHz and 900 MHz spectrometers. The 89 mm wide-bore 750 and 600 MHz spectrometers are available for solid-state NMR studies. The 800 MHz spectrometer is equipped with solids capabilities as well. All spectrometers are fully equipped with hardware for modern, state-of-the-art multinuclear experiments, including gradient probes and the capability for multi-channel pulsing with deuterium decoupling. Cryoprobes have been installed at every field strength except 750 MHz.

The NMR facility manager is Mike Delk.Nuclear Magnetic Resonance (NMR) spectroscopy

The seven spectrometers are:

1)  Bruker-BioSpin Avance II+ 900 MHz NMR Spectrometer

2)  Bruker-BioSpin Avance II 800 MHz NMR Spectrometer

    2.2k degree actively shielded 54mm bore super conducting magnets.
    34 gradient orthogonal shim systems.
    Variable temperature control.
    5 channel operation.
    Advanced digital receiving / digitizing capabilities
    Linux based PC control workstation.
    5mm HCN triple resonance cryoprobe yielding ultra-high sensitivity.
    13C observe capability with increased sensitivity.
    Conventional high resolution probe(s).
    Solids and HRMAS capability (800 MHz).
   
3) Bruker-BioSpin Avance 700 MHz NMR Spectrometer

4) Bruker-BioSpin Avance III HD 600 MHz NMR Spectrometer #1

5) Bruker-BioSpin Avance II 600 MHz NMR Spectrometer #2

    4.7k degree actively shielded 54mm bore magnets.
    34 gradient orthogonal shim systems.
    Variable temperature control.
    5 channel operation.
    Advanced digital receiving / digitizing capabilities.
    Linux based PC control workstation.
    5mm HCN triple resonance cryoprobe yielding ultra -high sensitivity.
    13C observe capability with increased sensitivity.
    Conventional high resolution probe(s).

6) Bruker-BioSpin Avance 600 MHz wide-bore NMR Spectrometer

7) Bruker-BioSpin Avance III HD 750 MHz wide-bore NMR Spectrometer (Click here to visit the 750wb information page)
    4.7k degree actively shielded 89 mm bore magnet.
    28 or 34 gradient orthogonal shim system operation.
    Variable temperature control.
    4 channel operation.
    Solid-State NMR (CPMAS, Static and HRMAS).
    Ultra-low temperature Magic Angle Spinning equipped.

High Performance Computing (HPC)

High Performance Computing systems for structural calculations consist of two symmetric multi-processor systems, 1 Tesla GPU system, and two Beowulf clusters running the Linux Operating System.

SMP Systems

**Executor:  This 56 core computer consists of 4 12-core 2.6Ghz Xeon CPU’s and has 256GB of shared memory for processing that needs to utilize large blocks of memory at once.  The machine also has 2TB of SSD local disk space for ultra-high speed local processing.

Chimera:   This 48 core computer consists of 4 12-core 2.1GHz Opteron 6172 CPUs and has 192GB of shared memory for processing that needs to utilize large blocks of memory at once. The machine also has 400GB of local disk space.

GPU Systems

Archer:  This 48 core computer consists of 2 24-core Intel Xeon CPUs and has 256GB of shared memory for processing that needs to utilize large amounts of memory and GPU accelerated resources.  It has two Tesla K40 GPU's for a total of 5760 compute cores running at 875MHz and 24GB of GPU memory.  The machine also has 1TB of ultra-fast solid-state local scratch space.

Beowulf Clusters

Ultron:  Ultron consists of 10 1U compute nodes and a 3U head node with solid-state storage.  Compute nodes have dual 14-core 2.4GHz Intel Xeon E5-2680 CPU’s with 256GB RAM.  All compute nodes have 512GB SSD drives as system/scratch space.  Two nodes contain NVidia Tesla K80 processors for CUDA accelerated applications.  Cluster communication is via a 56 Gb/s FDR InfiniBand.  In total there are 280 Xeon CPU cores with 2.56TB of RAM, and 9984 GPU/CUDA cores with 48GB GDDR5.  It has a theoretical peak performance of 28.212 TFLOPS for CPU's/GPU's combined.

DS2 (Deathstar II):  DS2 consists of 15 1U compute nodes and a 3U head node. Ten compute nodes have dual 12-core 2.6GHz opteron 6344 CPUs with 64GB of RAM while the other 5 have quad socket 12-core 2.1GHz opteron 6172 CPUs with 192GB of RAM. All Compute nodes have 400GB hard drives as system/scratch space. Two 24 core nodes also contain one GTX670 GPU card for CUDA calculations. The cluster is tied together using 10gigabit ethernet running at full duplex with jumbo frame rates enabled. In total there are 480 Opteron cores and 1.6TB of RAM. It has a theoretical peak performance of 2.256 TFLOPS for CPUs alone.