Structural Biology Core

Mission

The primary mission of the Structural Biology Facility is to provide 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 facilitates 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 electron microscopes and detectors, suitable for single particle analysis and imaging by CryoEM on the Evanston campus. In addition, the Facility provides crystallization robotics and analysis tools, and computational resources for analyzing data produced by 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 LS-CAT
  • Robotics equipment for crystallization experiments
  • UV crystal imaging capabilities
  • Software for structure analysis
  • Graphics facilities for visualization/presentation of molecular structures
  • Computer servers specialized for structural biology calculations
• Support and Training
  • X-ray crystallography, from designing crystallization experiments to structure determination and refinement
  • Molecular graphics for analysis and presentation
  • CryoEM and EM training

Resources Available

• Crystallography
  
  • Art Robbins, Inc. Phoenix and Gryphon crystallization robots
  • TTP Labtech Dragonfly liquid handler for crystal tray setup
  • Jansi UVEX UV/Vis microscope/imaging system
  • Stereomicroscopes (camera equipped, at room temperature and 4 degrees C)
  • Incubators for temperature-controlled crystallization
  • Coordination of access to LS-CAT for Northwestern University users
• CryoEM
  • Glacios™ Cryo TEM equipped with a Gatan K3 Direct Electron Detector
  • JEOL 1400 with Gatan 4k x 4k Ultrascan CCD camera
  • Solarus Plasma Cleaner and Pelco easyGlow™ Discharge Cleaning System
  • Cressington 308R carbon coater
  • Gatan Cryoplunge 3 and FEI Vitrobot Mark IV
  • Gatan 626 cryoholders with 655 Turbo pump stations
• Computational
  • 50+ node cluster running Linux including several single- and multi-GPU nodes
  • 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)
  • LTO6 writers for quick data backup
  • 45 tape LTO6 system for continuous data backup
  • Over 200 Tb of disk storage including RAID systems
  • 10 Gigabit fiber Ethernet connection to APS
• Software (representative examples)
  • Crystallography
    • CCP4 suite
    • PHENIX
    • SHARP
    • SOLVE
    • HKL2000
    • XDS
  • CryoEM
    • CryoSparc
    • Relion3
    • Leginon
    • cisTEM
    • Appion
  • NMR
    • CNS
    • FELIX
    • Aria
  • Modeling, graphics, and simulations
    • COOT
    • Pymol
    • Chimera
    • APBS
    • GROMACS
    • AMBER
    • VMD/NAMD
    • AlphaFold