- 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
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
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.
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
- Pucks (10) and tools for shipping up to
120 frozen crystals (compatible with Rigaku ACTOR™ crystal
mounting robot at ALS beamline 4.2.2).
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
- Saturn 724 HG CCD x-ray area detector.
- Workstation with HKL-3000R data
processing / structure determination software.
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.
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
- 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.
- 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
- Analysis: APBS.
For usage contact