Structural Biology Facility

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.

Contact Us

Director

Alfonso Mondragon, PhD

Services & Equipment

Key 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 Glacios™ Full Sample Evaluation - Fee for Service option to have initial sample evaluation performed by facility staff

Equipment

Synchrotron Crystallography (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 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 (fourth 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, 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
Glacios™ Cryo TEM equipped with a field emission gun capable of operating at 200 kV and outfitted with an AMETEK Gatan K3 Direct Electron Detector.
Solarus Plasma Cleaner

Computational (Chicago Campus, 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

Computational (Evanston Campus, fourth 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.

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

If K3 detector was used:

We acknowledge the use of the Ametek K3 direct electron detector, which was generously provided by Professor Robert A. Lamb, Ph.D., Sc.D., HHMI investigator

Core Navigator

For guidance on which cores may be most useful for your research and to coordinate use, please contact Core Navigator Sara Fernandez Dunne at s-fernandez@northwestern.edu or 847.491.5960.