Self rotation is not very clear - and the top peaks are almost certainly
generated partly by the high crystallographic symmmetry.
Things to check:
1) native Patterson - is there a non-crystallographic translation?
ctruncate checks this for you.
2) twinning - if there is a
Dear supervisors and potential candidates,
There is a vacant Ph.D. student fellowship available in the Biostructural
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I may have missed the original question, but the significance of
VdW interactions in general should hugely depend on the context.
Let's say, I would expect VdW in protein interfaces to have little
effect, because it gets compensated, on average, by VdW with water
molecules in dissociated state.
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Dear all,
a new version of mtz2hkl is available. Previous versions only wrote HKLF3
format if the data were amplitudes. The option '-2' now converts
amplitudes into intensities (and takes care of the standard deviations,
too).
The conversion of
REMINDER: APPLICATION PROCEDURE FOR PROPOSALS FOR BEAMTIME ON THE ESRF
Bio-SAXS BEAMLINE ID14-3
The new Bio-SAXS beamline at ID14-3 at the ESRF (
I was hoping people could give some tips on the best way to go about
crystallizing a protein-DNA complex.
I have a large amount of experience in protein crystallisation but have
never tried co-crystallisation with DNA until I started this project.
If you want to reply to me personally I will then
Hi Clare,
Two papers that might be worth checking out that address some of your
questions -
1. Tan et al, Crystallization of the Yeast MATa2/MCM1/DNA Ternary Complex:
General Methods and Principles for Protein/DNA Cocrystallization J. Mol.
Biol. (2000) 297, 947±959
2. Cannone et al,
1. Do people routinely try different lengths of DNA?
Yes, its usually the most important variable because the ends
like to stack against each other to form a pseudo-continuous
helix.
2. Do you start with blunt or sticky ends?
Both. Plan on a dozen or so different duplexes to start
Dear Clare et al:
The absolute classic paper in the field is this:
Schultz, S. C., Shields, G. C. Steitz, T. A. (1990).
Crystallization of Escherichia coli catabolite gene
activator protein with its DNA binding site. J. Mol.
Biol. 213, 159–166.
I've learned more from this than from reading
Postdoctoral position available:
Applications are invited for a postdoctoral position to investigate
the structure and biochemistry of proteins involved in Gram-negative
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Dear All:
Next week we are going to try some seleno-Met labeled crystals.
We checked the literature to try to find out the peak wavelength that has
been used for SAD or MAD data collection. But they are slightly different ( may
be 50 ev) in different papers.
I guess this is
I think scans are better than theory, and there can also be white lines which
are often dramatically higher than predicted. Just make sure that you do not
roast your best crystal when you do your scan!
Jacob
***
Jacob Pearson Keller
Northwestern
Always take the scan results ahead of the typical values unless they are
obviously wrong. Only use the predicted values if the scan is broken
or too weak (e.g. very small crystals) and in that case I'd be tempted
to add 10-20 eV to the typical peak wavelength to make sure you
weren't actually
Just checking my oxidized Se-Met experiments, I have 12658 to 12661 eV
for my peak energies, and 3 eV lower for the inflection.
As others have said, do the fluorescence scan. Use your experimentally
determined values.
Engin
On 7/16/09 11:54 AM, Phil Jeffrey wrote:
Always take the scan results
I second Phil's opinion - it is better to scan and be sure - as long as
the scan results are not hideously abnormal. If you cannot scan for
whatever reason but are sure that the X-ray optical system is properly
calibrated - then use Phil's numbers below :)
Artem
Always take the scan results
On Thursday 16 July 2009 10:15:51 Jerry McCully wrote:
Dear All:
Next week we are going to try some seleno-Met labeled crystals.
We checked the literature to try to find out the peak wavelength that
has been used for SAD or MAD data collection. But they are slightly different
On a different note,it seems as if SeMet is not a regular experiment
in your lab. So I would recommend not to burn your crystals and rather
sacrifice the resolution versus loosing your SeMet anomalous signal
after couple of degrees into the data collection. It would also be
wise to run
My 2 cents:
Cent #1 But they are slightly different ( may be 50 ev) in different
papers. This statement itself contains the answer - always scan, but it
was already suggested by many. I'd like to get to slightly different
issue here. No oxidation or any other interaction in protein crystals
FYI, for folks not subscribed to pymol-users:
nVidia today released beta drivers which at last enable OpenGL-based
stereo 3D visualization on 120 Hz LCDs using Quadro graphics cards. So
long as you are willing to put up with Windows, you can finally abandon
those old CRTs without spending a
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