Biomolecular Structure Laboratory

The Chapman group manages resources for the determination of atomic structure by X-ray crystallography:

Incubators and microscopes for crystallization of biomolecules.
Instrumentation for (on campus) collection of x-ray diffraction data.
Access to synchrotron beamline 4.2.2 at the Advanced Light Source (Berkeley) for high-intensity / multi-wavelength x-ray data collection.
Computers for data processing, analysis and molecular modeling.

On-campus resources are located in room 533 of the Medical Research Building. Instrumentation has been purchased through a grant from OHSU, with on-going support from OHSU's department of Biochemistry & Molecular Biology, and through the grants of participating research groups. We do our best to support the local community, with users from several departments at OHSU, Shriner's hospital, Portland State University and Reed College. Although increasingly automated, determination of macromolecular structure remains somewhat labor-intensive and requires some expertise. Those interested should consult with Michael Chapman to discuss what level of assistance would be required.

Crystallization:

The laboratory provides high capacity equipment with a low level of automation to complement the fully automated, lower capacity robotics in the Gouaux laboratory. Specifically, we operate two vibration-free incubators (4°C, 20°C) and a auto-stage microscope to facilitate the rapid evaluation of crystallization trials. These systems are compatible with crystallization trays of a number of formats that could be set up manually, or using multi-channel liquid dispensing robotics such as the Mosquito™ in the Gouaux laboratory. The incubators have essentially infinite capacity, providing an alternative to hotel/imaging systems, with the proviso that trays have to be manually loaded into our imaging system.

Molecular Dimensions MD-502 incubators (2): 250L; Vibration free temperature control 0°C to 50°C ±0.5°C (currently 4°C & 20°C).
Rigaku Minstrel™ DT: automated crystal imaging workstation, including optics with polarized light at a resolution of 5μm. Supports bar-coded tracking of trays, and remote access of an image database.

Crystal handling:

The laboratory has a dissecting microscope for crystal-mounting either in the diffraction laboratory or the cold room, and tools / dewars for the cryo-freezing of samples and shipping to the synchrotron.

Nikon SMZ 745T dissecting microscope for sample-mounting; halogen light source.
Leica S6D dissecting microscope with halogen light source, polarization, and CCD camera attachment for documentation (in Chapman lab, MRB 534).
Dry dewars for shipping to the synchrotron (2).
Pucks (10) and tools for shipping up to 120 frozen crystals (compatible with Rigaku ACTOR™ crystal mounting robot at ALS beamline 4.2.2).

X-ray diffraction:

$OHSU diffraction instrumentation.$ The laboratory runs a Rigaku Compact HomeLab™ system that is suitable for: (a) complete data collection with well-behaved samples; (b) preliminary screening of crystals; (c) phasing using the sulfur anomalous scattering with strongly diffracting crystals. The system has the following components:

MicroMax-003 sealed tube x-ray generator operated at 50 kV x 0.6 mA with integral confocal optics providing a 100μm beam diameter at the crystal.
4-circle goniostat allowing for optimally-efficient crystal orientation, and detector offset for high resolution data collection.
Oxford CryoStream™ 700 crystal cooling (from Gouaux lab.), now with an Oxford CryoSystems AD51 dry air stream.
Saturn 724 HG CCD x-ray area detector.
Workstation with HKL-3000R data processing / structure determination software.

Synchrotron beamline:

OHSU is a member of the Molecular Biology Consortium (MBC), based at the Advanced Light Source (ALS) in Berkeley, CA. Through OHSU's initial capital investment and continuing contributions to the upkeep from the Department of Biochemistry & Molecular Biology, as well as individual investigators, the department maintains a 10% share of the facility, giving it access to 10% of the 75% of beam-time allocated to member institutions. Support is provided for on-site data collection, or rapid access through samples shipped to the beam-line, with either automated data collection, or experimental control through the internet. Features offered by the beam-line include:

Automated crystal mounting / screening using a Rigaku ACTOR™ crystal mounting robot.
Support for small, weakly-diffracting crystals with high intensity beam.
Support for MAD / SAD / SIRAS phasing experiments using a beam of variable wavelength.

Computational:

The laboratory operates a compute server comprising that is being used by several groups for structure determination as well as computer simulation / modeling:

4 x 8-core server with 2.2 GHz Intel X7560 hyperthreaded processors (32 core; 64 thread) with 24 MB cache.
2 x NVIDIA C2050 448 GPU CUDA floating point array processors.
128 GB RAM.
10 TB RAID-1/RAID-5 disk storage; nightly backup to 12 x LTO-5 tape system.
Software:
- Crystal structure determination: HKL-3000, CCP4, CNS, Phenix.
- Electron microscopic structure determination: EMAN(2), Spider, RSRef.
- Molecular modeling: CHARMM, NAMD (VMD), Chimera, Modeller, PyMol.
- Quantum mechanical: G09 (Gaussian), NBO.
- Analysis: APBS.

For usage contact Andrew Trzynka.


by Michael S. Chapman