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Protein Crystallography Newsletter
Volume 1, No. 5, June 2009
In this issue:
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Continuing Education Webinar
Maintenance for a MicroMax-007 / 007
HF
rotating anode X-ray generator.
Presenter: Adam Courville
July 16 at 12:00 PM EDT (16:00 GMT)
Click
here to register |
MicroMax™-007 HF microfocus X-ray generator (top) and as part of the
Rigaku Highflux HomeLab system (bottom).
Bookmark PXUniverse.com
as your portal to the world of protein crystallography.
Illustration of how collecting data in 1x1 binning
mode can help resolve diffraction spots.
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Crystallography in the news
June 24, 2009. Dutch software to weed out errors in
Protein Data Bank. Protein structures are getting regular makeovers with
the help of 're-refinement'
software developed by Dutch structural biologists.
June 16, 2009. New research by scientists at The Scripps Research
Institute and other institutions provides a close-up look at the
cone-shaped shell that is the hallmark of human
immunodeficiency virus (HIV), revealing how it is held
together—and possible ways to break it apart.
June 16, 2009. The 2009
Carl Brändén Award was presented by Paul N. Swepston, Ph.D.,
President and General Manager of Rigaku Life Sciences, to Dr.
Bruce Alberts (University of California, San Francisco and
editor-in-chief of the journal Science) for his national and
international commitment to the promotion of educational principles as
well as the "creativity, openness and tolerance that are inherent
to science."
June 11, 2009. Howard Hughes Medical Institute researchers are reporting
the first detailed molecular snapshots of a deadly gastrointestinal
virus as it is caught in the grasp of an immune system molecule with the
capacity to destroy it. HHMI investigator Stephen
C. Harrison and colleagues mapped the structure of an antiviral
antibody clamped onto a protein called VP7 that stipples the surface of
rotavirus.
Better
performance AND less maintenance
Since the introduction of the first sub-100 micron
rotating anode in 2002, hundreds of Rigaku microfocus generators have
been installed in protein crystallography labs around the world. The
current model MicroMax-007
HF
delivers performance comparable to a second generation beamline. The most
challenging projects can now be performed in the home laboratory: screen
crystals where no diffraction is seen on a standard system, collect full
data sets on samples where only low resolution reflections would
normally be observed, and solve previously intractable structures.
Contrary to intuition, higher performance does not mean higher
maintenance. The MicroMax-007 HF actually requires less maintenance and service
than its predecessors. Engineering design improvements have lengthened
the time between routine service and made it easier and faster to
perform maintenance. Featuring a unique and reliable direct-drive anode,
the MicroMax-007 HF
compact tower assembly contains both the vacuum chamber and
turbo-molecular pump for fast pump downs. Pre-mounted, pre-crystallized
filaments allow users to change filaments in a few minutes so they can
quickly get back to collecting data.
Dramatically improved filament lifetimes, and anodes that only require
maintenance about once a year, allow you to spend more time screening
crystals and collecting data and less time on maintenance. When you do
need to change the anode, customers can quickly swap out the old anode
with a freshly rebuilt one. To maximize uptime, customers can purchase
two anodes and sign up for our Anode Storage Program — where
we will ship you a freshly rebuilt anode when you need one so that you
don't need to wait for your anode to be rebuilt.
Request a copy of the MicroMax-007
HF
brochure or ask for more information about the Anode
Storage Program.
Maintenance
for a rotating anode X-ray generator
Rigaku
Life Sciences Webinar Series continues on July 16th with a
discussion on maintenance and routine service for microfocus rotating
anode X-ray generators. Hosted by analytical X-ray systems specialist
Adam Courville, this complementary continuing education seminar is
recommended viewing for any MicroMax-007 or 007HF users and for people
interested in learning about what maintenance is required for a
state-of-the-art rotating anode generator.
Click
here to register.
Useful
links for crystallography
The 2009 Dorothy Crowfoot Hodgkin Award, sponsored by Genentech and
granted in recognition of exceptional contributions in protein science,
was presented to Dr.
Janet Thornton (European Bioinformatics Institute) on June 15, 2009
for her pioneering work in the field of bioinformatics. Thorton's lab
offer several web based tools to aid in the analysis of protein
structures:
ProFunc
- for analysis of a protein's 3D structure to help identify its likely
biochemical function.
Catalytic
Site Atlas - obtain catalytic residue details.
PDBsum
- provides an at-a-glance overview of every macromolecular structure
deposited in the Protein Data Bank (PDB), giving schematic diagrams of
the molecules in each structure and of the interactions between them.
Selected
recent crystallographic papers
The p22 tail machine at subnanometer resolution reveals the
architecture of an infection conduit. G.C. Lander, R. Khayat, R. Li,
P.E. Prevelige, C.S. Potter, B. Carragher and J.E. Johnson.
Structure 17,
No. 6, 789-799 (2009).
Structure and mechanism of an amino acid antiporter. Xiang Gao, Feiran
Lu, Lijun Zhou, Shangyu Dang, Linfeng Sun, Xiaochun Li, Jiawei Wang and
Yigong Shi. Science 324,
No. 5934, 1565-1568 (2009).
Cellular mechanisms of membrane protein folding. William R. Skach.
Nature
Structural & Molecular Biology 16, No. 6,
606-612 (2009).
Crystal Structure of the sodium-potassium pump at 2.4 Å resolution. T.
Shinoda, H. Ogawa, F. Cornelius and C. Toyoshima.
Nature 459,
446-450 (2009).
FAQ:
How to get better spot separation and data
When diffraction spots are too close together, it
implies that your detector is too close to the sample and/or your
crystal has a long unit cell axis. There are several experiments you can
do to test for optimal data collection parameters which will result in
better separation between spots. One common sense way is to increase the
crystal-to-detector distance. This usually helps unless you have a
highly divergent optic in which case you want to try and keep the
detector as close to the crystal as possible.
A second approach is to either collimate the beam or, in the case of
VariMax optics, close the slits a bit. Both of these options have the
disadvantage that you will also decrease the flux on your crystal which
will result in the need for longer exposure times.
Another method you can easily try is to collect images in unbinned (1x1)
mode. The usual default bin mode for most CCDs is 2x2. As the image (at
left) illustrates, finer sampling of the detector space with unbinned
images can sometimes resolve spots. More likely than not, if you have a
challenging system you will need a combination of these techniques. And
if all else fails at home, there's always the synchrotron.
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