Hi All,
This is a bit off topic I guess. The system I am using is a dual-boot
system with Windows 8 and Ubuntu 12.1 installed. I am running CCP4 in
Ubuntu in a shared folder (File system: NTFS) with windows. Before this
morning, everything was fine except that the system could not read
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Dear Kok Lian,
can you run a filesystem check from the windows side? I don't know the
current status of the NTFS driver in Linux, but it used to be quite
broken (unsurprisingly, given NTFS ;-) and I would not write data on
an NTFS partition using
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Dear all,
I am looking for a tool that prints (and preferably plots, e.g. as
postscript) the pairwise anomalous CC vs. resolution for several input
HKL-files.
xprep does this, but it is interactive and requires a fair bit of
typing. Since I have a
Hello Tim :-)
You can try to do this with sftools. It is also an interactive type of program
input but you can easily calculate correlations. After converting xds files to
mtz, you can try some thing like this :
sftools eof sftools_1.log
READ $mtz1
READ $mtz2
SELECT RESOL 2.8
CORREL COL 5
If you assigns them to different datasets in Pointless, then Aimless will give
you the cross-dataset correlations. By default it will scale them to together
first, but you can skip that if you want
It might not scale well to a large number of files (OK up to about 10 I guess)
Phil
On 14 Mar
Dear all,
Find enclosed the last call for the Summer School on Integrated Biology to be
held next July in the French Alps.
Best regards,
Isabel
Début du message réexpédié :
De : Eva Pebay-Peyroula eva.pebay-peyro...@ibs.fr
Objet : [ibs.tous] Les Houches SUMMER SCHOOL LAST CALL
Date : 14 mars
Hello everyone,
I have a query for the scientists working on protein-protein interaction.
It is known that some proteins exist in unfolded or molten globule state
and attain structure on interaction with other folded proteins.
Many a times, it is difficult to obtain the structure of these
New Frontiers in Neutron Macromolecular Crystallography Workshop
Oak Ridge National Laboratory
Spallation Neutron Source
USA
July 15-16, 2014
This meeting will bring together scientists to discuss new
opportunities for research at the two advanced neutron user facilities
(SNS and HFIR) at
Hi Stefano,
On top of all that has been suggested you should also be aware of the effect of
pH and buffer composition on the apo-holoenzyme equilibrium during purification
and crystallization.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Hi,
I think the experiment is doable, but how would you decouple
protein-protein interaction from folding of the unfolded
protein due to protein interaction?
Reza
Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY
Stefano,
Before you address the problem, you need to ask yourself a couple of things.
You say that on the gel filtration we clearly see two bands corresponding to
holoprotein and free FAD. That is not too odd, but have you ask the question
is all the protein good protein.
Is this an
That is a very interesting question, which I would request the seniors out
there to give their insights on.
I was imagining that a recombinant purification of an unfolded partner
would aggregate which would cause trouble in ITC. Am I correct in this
theory?
Would love to have more insights.
Dear Stefano,
Here few thoughts:
You should calculate the amount of holo/apo protein that you get after the
column. A ratio 280/450 between 9-12 it will suggest that your protein is
almost completely in the holo-form. So, I will be worried about the peak of
flavin only if this ratio become
Dear Anita
One alternative method to determine the thermodynamics and potentially discern
the folding energy changes from the interaction driven ones would be NMR.
Advantages over ITC experiments include: determine if the interaction drives
foldness, estimate associated thermodynamics and, if
I have done once by using two proteins, one is disordered, the other is very
well folded. The result I got is the baseline drift. The baseline goes up upon
each injection. The reason I thought at that time is the heat capacity changed
dramatically in the system. The disordered protein may form
One of my main concerns is that the unfolded protein itself would irreversibly
aggregate and then wouldn't interact with the folded protein. I think DSC
(differential scanning calorimetry) should be performed first to characterize
the state of both proteins and their potential complex. By
If the twin law is k,h,-l, then your a axis must almost equal the b axis?
And if the twin fraction is 0.48 then you have additional symmetry I guess?
How sure are you that the point group is P4/mmm?
On 13 March 2014 20:41, Teresa Swanson teresa.m.swan...@gmail.com wrote:
Dear collegues,
Le Vendredi 14 Mars 2014 13:37 CET, Anita P crystals...@gmail.com a écrit:
Anita,
If one of the partners is indeed more or less unfolded before interaction,
then you should see a negative DeltaS upon complex formation.
Practically, I would try first putting the unfolded protein in the cell
An Fo-Fc map is actually the real-space representation of the Fo-vs-Fc R
factor (Rcryst), so the sigma of this map will continue to drop
relative to the true electron scale as your model improves and the
difference between Fo and Fc diminishes. The 2Fo-Fc map, however, is a
best guess of the
At the limit, the microdomain picture leads to powder-diffraction-type spots
(rings), provided the block size is relatively large with respect to the unit
cell. And as the blocks get smaller, the distinction between changing unit
cell parameters and mosaic block misorientation dissolves.
I am
Dear All
On similar lines any suggestions and tips on expression and
purification of the proteins containing both FAD and NADPH would be really
helpful.
I recently tried to express and purify a protein containing these two
ligands, but failed (aggregation of protein).
my initial questions
Hi Teresa,
As Eleanor has mentioned, you should probably check out other space
groups. Xtriage gives a lot of great information and many plots to
inspect. But, if you do not know what the plots mean and just look at
the results that say the twin fraction is 0.48 you can get into some
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