Hi ,
I am co-crystallizing a protein with compound and would like to know how much
of compound to add to protein solution to start with. I know that the protein
binds compound in a 1 to 1 ratio but also noticed that the compound
precipitates out of solution when DMSO is diluted off. Where
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for me, I prefer to sock these compounds into your crystal. it will much more
easy than co-crystallizaiton. But each protein should be different.
Normally when I star to co-crystallization with small compound, I will set up
the complex with 1:1.2 molar ratio as first trial to see what should
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Hello Ian,
I dare say that the goal is to get phases which match as good as
possible with what is inside the crystal. If this coincides with
maximising the likelihood, why don't we run refinement until the LL
stabilises?
@Garib: I have seen runs
Did you rename the ligand in the CIF file as well? It would be nice if the Prodrg interface allowed you to type in the
name of the ligand you want in the CIF and PDB file. Hopefully a global replace in your favourite text editor of DRG
with LIG or whatever you want to call your ligand would
Dear,
We're wondering what tools there are available in order to estimate
the 'melting point' and 'heat of fusion' from a known crystal
structure (e.g. coordinate file)..?
It concerns mostly small molecules ( 100 atoms).
Many thanks
Kristof
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Kristof Van
Hello Tim
It was in one or two versions and I did not get consistent results. However
code is there and I can activate it if you want. If you know what criteria you
would like to use I can code that also.
In some cases it happens that R/Rfree go up and then they start coming down. It
may be
Hi all,
Thanks for the suggestions! Anyway, the problems have been fixed! When I
edited the CIF files in a mac editor, the file formatting got changed, so a
line feed became a carriage return and Coot does not like this as to it they
appear to be different files.
The CIF files were fixed by using
TIm,
I dare say that the goal is to get phases which match as good as
possible with what is inside the crystal. If this coincides with
maximising the likelihood, why don't we run refinement until the LL
stabilises?
That's exactly what you should do: any optimisation procedure attains the
Hmm, I used to think I understood this, but I'm feeling a bit dim right
now.
On 25/08/2011 11:07, Ian Tickle wrote:
Since the target function in MX refinement is the total likelihood
(working set + restraints), there's no reason whatsoever why any
another function, such as Rfree LLfree,
Hi Frank
This is self-evident; what is not obvious is why the target function
should be having the final word. Wasn't the word over-refinement
introduced to describe exactly this: that the target function was wrong?
I assumed people were confusing 'over-refinement' with 'over-fitting'; there
Hi all,
I have a large disordered loop (33aa) for a 2.0 Å dataset for which the rest of
the structure is well-defined, and phases are decent (Rwork=19.6, Rfree=24.6).
I can see some broken up density at one end, but have been unable to
convincingly build into into this region manually. I would
Hi YT-
We normally prepare our ligand stocks in DMSO and add this to the protein in
3-fold molar excess. The majority of our ligands are quite insoluble and
precipitate when the DMSO concentration decreases upon addition to the
protein... so I am not surprised that you are seeing this.
Dear TY,
Typically between 5-10x molar concentration over the protein is enough to
ensure binding when the IC50 is uM to low mM. For tighter binding compounds (nM
to low uM), 2-5x is sufficient. Whatever you do, when the precipitate occurs DO
NOT REMOVE it. I learned to my chagrin that you
Calculate - Merge Molecules
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
jab
Sent: Thursday, August 25, 2011 4:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] merge chains in coot
Hi
I've tried to find where to merge chains in coot,
Time to start digging in the archives. Try looking at work by Fran
Jurnak in 1986 (J. Cryst. Growth 76, 577) and Bill Ray's work in 1985
(Analytical Biochem 146, 307), and then the works that cite them. I
thought this was common knowledge, but I guess it goes in phases.
Aging of
Dear Greg,
Try ARP/wARP 7.2, released a few days ago, which is better, more
stable and should have improved flash of error messages to the log
files.
ARP/wARP Loopy will not build a 33-residue loop at once, but Classic
model building may get the gap shortened.
Go to www.arp-warp.org
Dear All
I quick reminder - last chance to sign up for the 2nd MX User Workshop at
Diamond - the workshop is part of the Synchrotron User Meeting, September
7th-8th, 2011. Workshop sessions include presentations from staff and users on
latest developments, spectroscopy, crystal dehydration and
Successful complexation depends on the
concentration of protein, ligand, and the Kd of the protein-ligand
complex. For Kd[protein], you will probably require
[ligand] 10 x Kd. As Kd approaches [protein], slightly
superstoichiometric quantities will be sufficient for
Dear colleagues,
I would like to draw your attention to an upcoming free, educational webinar to
be presented by Jim Pflugrath, Ph. D. titled An Insider's Guide to
CrystalClear and d*TREK: Improve Your Results with these New Features and
Tips. In this webinar, Jim will discuss three important
Hi Ian
(Yes, your technical point about semantics is correct, I meant
over-fitting.)
To pin down your points, though, you're saying:
1) Don't use Rfree, instead look at LLfree or Hamilton Rfree.
2) Compare only the final values at convergence when choosing
between different
Point #2 would hold if we routinely let our refinements run to
convergence; seems common though to run 10 cycles or 50 cycles instead
and draw conclusions from the behaviour of the metrics. Are the conclusions
really much different from the comparison-at-convergence you advocate?
Which is
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