Northwestern University Feinberg School of Medicine
Research

Structural Biology Core

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 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 a large group of users by providing regular 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 robotics and analysis tools, 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. The Structural Biology Facility also serves to nucleate the development of a supportive local community with expertise in structural and computational biology.

Services Offered

Macromolecular Structure Determination and Analysis

  • 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, 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

Support and Training

  • Expert consultation in crystallography, CryoEM and Computational Support
  • X-ray Crystallography, from designing crystallization experiments to structure determination and refinement
  • Computational drug design and structural simulations
  • Molecular graphics for analysis and presentation
  • CryoEM and EM training to potential users, support ranging from specimen development, specimen preparation, and imaging to computational image analysis and full sample evaluation

Equipment Available

Synchrotron Crystallography - Advanced Photon Source, Sector 21, LS-CAT

  • 1 Eiger Dectris 9M continuous readout detector (21-ID-D)
  • 2 Rayonix MX-300 mm (21-ID-D and 21-ID-G) CCD detectors
  • 1 Rayonix MX-225 mm (21-ID-F) CCD detector
  • 4 Cryogenic Automated Transfer System (CATS) Robotic sample changers
  • 4 Oxford cryojet liquid nitrogen cryocooling systems
  • 4 MD2 microdiffractometers
  • Numerous Pentium PCs running Linux for instrument control, data processing, and for structure determination and refinement
  • 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

  • Art Robbins, Inc. Phoenix crystallization robot
  • Jansi UVEX UV/Vis microscope/imaging system
  • Stereomicroscopes (camera equipped, at room temperature and 4 degrees C)
  • Incubators for temperature-controlled crystallization

  Evanston Campus

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

CryoEM

  • 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
  • JEOL 1400
  • Gatan 4k x 4k Ultrascan CCD camera
  • Orious 1000 CCD
  • Solarus Plasma Cleaner
  • Cressington 308R carbon coater and thickness monitor
  • Cryoplunge 3
  • Gatan 655 Turbo Pumping Station

Molecular Characterization
  Chicago Campus

  • Tecan Safire2 multimode, multiplate reader (UV/Vis, Fluorescence, Luminescence)

Computational

  Chicago Campus

  • 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
  • 10 Gigabit fiber Ethernet connection to APS

  Evanston Campus

  • 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

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, CNS, SHARP, and SOLVE, and X-ray diffraction data processing programs HKL2000, XDS and MOSFLM. For NMR we support CNS, FELIX and Aria. We support molecular graphics software for model building, analysis and presentation including O, MIDAS, Molscript, Raster3D, RasMol, WHATIF, XtalView, Quanta, COOT, Turbo Frodo, Pymol 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:

"We acknowledge staff and instrumentation support from the Structural Biology Facility at Northwestern University, the Robert H Lurie Comprehensive Cancer Center of Northwestern University and NCI CCSG P30 CA060553."

If K2 detector was used: "The Gatan K2 direct electron detector was purchased with funds provided by the Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust"

Structural Bio Home Page

Contacts

Pamela J. Focia, PhD  
Facility Manager

(312) 503-0848

Alfonso Mondragon, PhD  
Director


Locations

Computational

Ward/Searle buildings, 7th & 8th Floors
303 E. Chicago Avenue
Chicago

Cook Hall, 4th Floor
2220 Campus Drive
Evanston 

Crystallography and molecular characterization

Ward building, 7th Floor
303 E. Chicago Avenue
Chicago

Cook Hall, 4th Floor
2220 Campus Drive
Evanston

Advanced Photon Source

Northwestern University is a founding member of the Life Sciences Collaborative Access Team (LS-CAT), located at Sector 21 of the APS, at Argonne National Laboratory, 30 miles southwest of Chicago