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Structural Biology Facility

Mission:

The primary mission of the Structural Biology Facility is to provide state-of-the-art equipment, training, technical support, and maintenance of equipment indispensable for structural biologists and other researchers studying the structures of biological macromolecules and materials. The Facility also provides structure determination and data collection services, both for crystallography and cryoEM.

The Facility plays an essential role in the research programs of investigators who are studying the relationship between macromolecular structure and function, using macromolecular structure as the starting point for structure-based drug design, or needing to characterize complex biomaterials. It is a unique resource at Northwestern University that capitalizes on the extensive expertise of its Facility Managers to provide access and support for experiments using the synchrotron radiation X-ray source at the Life Sciences Collaborative Access Team (LS-CAT) beamlines at the Advanced Photon Source (APS) at Argonne National Laboratory, and state-of-the-art electron microscopes and detectors, suitable for atomic-level structural studies by CryoEM on the Evanston campus.

In addition, the Facility provides crystallization robots and microscopes for analyzing crystallization experiments, all the equipment for sample preparation for EM studies, and computational resources for analyzing data produced by a wide range of experimental approaches — including crystallography, electron microscopy, and NMR — together with computational tools for modeling and design studies.

Services:

Support and Training

  • Macromolecular Crystallography, from designing crystallization experiments to structure determination and refinement
  • CryoEM 1:1 training for users, support ranging from specimen development, specimen preparation, and imaging to computational image analysis, and structure determination
  • Computational drug design and structural simulations
  • Molecular graphics for analysis and presentation

Macromolecular Structure Determination and Analysis, Crystallography

  • Support for macromolecular crystallography at the Life Sciences Collaborative Access Team (LS-CAT) at Sector 21 of the Advanced Photon Source at Argonne National Laboratory, including Remote Data Collection capabilities
  • Robotics equipment for crystallization experiments on both campuses, including membrane proteins in the lipidic cubic phase and in bicelles
  • UV crystal imaging capabilities on both campuses
  • Software for structure analysis (Crystallography, NMR, Cryo EM, Modeling, Simulations and Drug Discovery)
  • Advanced graphics facilities for visualization/presentation of molecular structures
  • Powerful servers to perform long and complex calculations
  • High-throughput fluorometric analysis of macromolecular interactions

Full Services Section

  • Expert consultation (Crystallography, CryoEM, Computational)
  • Structure determination and data collection services for crystallography and cryoEM
  • Opportunity for potential/active users of the facility to have 1:1 meetings with facility staff to discuss project related issues or to obtain extensive training
  • Full service structure determination by Facility Staff using X-ray crystallography techniques
  • JEOL 1400 Full Sample Evaluation - Fee for Service option to have initial sample evaluation performed by facility staff
  • CryoEM JEOL 3200 Full Sample Evaluation - Fee for Service option to have initial sample evaluation performed by facility staff

Equipment:

  • Synchrotron Crystallography

    Located at Sector 21, LS-CAT of the Advanced Photon Source, Argonne National Laboratory

    • 1 Eiger Dectris 9M continuous readout detector (21-ID-D)
    • 2 Rayonix MX-300 mm CCD detector (21-ID-G, 21-ID-F)
    • 1 Rayonix MX-225 mm CCD detector (21-ID-E - under commissioning)
    • 4 Cryogenic Automated Transfer System (CATS) Robotic sample changers
    • 4 Oxford cryojet liquid nitrogen cryocooling systems
    • 4 MD2 microdiffractometers
    • Numerous PCs running Linux for instrument control, data processing, and for structure determination and refinement
    • LUSTRE filesystems
    • DVD drives and firewire disks for data backup
    • Terabytes of disk space for data storage managed as a Lustre file system
    • TV monitors and cameras
    • Liquid nitrogen dewars
    • Assorted cryocrystallography equipment
  • In-House Crystallography

    Chicago Campus, located in Tarry 7-710

    • Art Robbins, Inc. Phoenix crystallization robot
    • Jansi UVEX UV/Vis microscope/imaging system
    • Stereomicroscopes (camera equipped, at room temperature and 4 degrees C)
    • Molecular characterization: Tecan Safire2 multimode, multiplate reader (UV/Vis, Fluorescence, Luminescence)

    Evanston Campus, located on the 4th floor of Cook Hall

    • Art Robbins, Inc. Gryphon crystallization robot (for both soluble proteins, and also for membrane proteins using the Lipidic Cubic Phase and bicelles)
    • Robomicroscope automated crystal imaging system
    • 2 Jansi UVEX UV/Vis microscope/imaging systems (one each at room temperature and 4 degrees C)
    • Stereomicroscopes (at room temperature and 4 degrees C)
    • Incubators for temperature-controlled crystallization
  • Cryo Electron Microscopy

    Evanston Campus, located in B509 Silverman Hall

    • Cressington 308R carbon coater and thickness monitor used to make carbon support films for TEM samples
    • Cryoplunge 3 for preparation of frozen hydrated specimens for use in the JEOL 3200 FS
    • Gatan 655 Turbo Pumping Station designed for TEM applications capable of producing a vacuum in the 5E -6 Torr range
    • JEOL 1400 120 KV electron microscope for sample evaluation
    • JEOL 3200FS TEM equipped with a in-column energy filter (omega filter) and a field emission gun capable of operating at 200 or 300 kV and outfitted with a Gatan K2 Summitt Direct Electron Detector.
    • Solarus Plasma Cleaner
  • Computational

    Chicago Campus, located in Morton 7-614

    • 2 Quad-core Intel Xeon 3.4GHz workstations (3D stereo equipped for visualization and model building)
    • DVD/CD writers for quick data backup
    • 20 tape LTO system for continuous data backup
    • Over 10 Tb of disk storage including RAID systems
    • Gigabit Ethernet connection to APS

    Evanston Campus, located on the 4th floor of Cook Hall

    • 24 node Xeon E5-2680/Pentium 4 Xeon/AMD Opteron cluster running Linux
    • 7 Quad-core Intel Xeon 3.4GHz workstations (3D stereo equipped for visualization and model building)
    • 3 Dual Quad-core Intel Xeon 3.5GHz workstations with GPU computing capabilities (3D stereo equipped for visualization, model building, and GPU computing)
    • DVD/CD writers for quick data backup
    • 45 tape LTO6 system for continuous data backup
    • Over 80 Tb of disk storage including RAID systems
    • 10 Gigabit fiber Ethernet connection to APS and to CryoEM microscope

Software:

We support a wide-variety of software for structure determination and analysis with identical computing environments on both the Evanston and Chicago campuses. Macromolecular crystallography software includes the CCP4 suite, Phenix, CNS, SHARP, and SOLVE, and X-ray diffraction data processing programs HKL2000, XDS and MOSFLM. For cryoEM we support appion, EMAN, relion, Spider, Xmipps and others. For NMR we support CNS, FELIX and Aria. We support molecular graphics software for model building, analysis and presentation including COOT, Pymol, MIDAS, Molscript, Raster3D, RasMol, WHATIF, XtalView, Quanta, and GRASP. We support modeling, simulations and drug discovery software packages including DOCK, AutoDock, GOLD, SYBYL, Allegro, Delphi, GROMACS, AMBER, AMSOL, MS, and INSIGHT/DISCOVER.

Acknowledgement

All manuscripts and grants presenting work supported by this core should include the following acknowledgement:

"This work used resources of the Northwestern University Structural Biology Facility which is generously supported by NCI CCSG P30 CA060553 awarded to the Robert H Lurie Comprehensive Cancer Center."

Contact:

Director:
Alfonso Mondragon, PhD
a-mondragon@northwestern.edu

Operations Director:
Valerie Tokars, Ph.D.
v-tokars@northwestern.edu

Location(s):

  • Advanced Photon Source - Life Sciences Collaborative Access Team - Sector 21
    • Located at Argonne National Laboratory, 30 miles southwest of Chicago
  • Crystallography
    • Tarry Building Room 7-710, 303 East Chicago Avenue, Chicago
    • Cook Hall, 2220 Campus Drive, 4th Floor, Evanston
      Facility Manager: Pamela J. Focia, PhD ( focia@northwestern.edu)
  • Computational
    • Morton and Ward Buildings, 7th & 8th Floors, 303 East Chicago Avenue, Chicago
    • Cook Hall, 2220 Campus Drive, 4th Floor, Evanston
      Facility Manager: Jason Pattie (j-pattie@northwestern.edu)
  • CryoEM
Phone:
847.491.5139