Dear Lionel,
In case of a lipid-binding protein, we were able to remove most (90%) of the
bound lipids with a lipidex column. This could be verified by DSF since the
melting temperature of lipid-bound protein was ~6°C higher as the melting
temperature of the free protein. The delipidated
PS: if you are working with a human protein: most human proteins are quite
stable at 37°C (for obvious reasons).
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Schreuder, Herman RD/DE
Gesendet: Freitag, 27. Juni 2014 09:21
An:
Hi,
I'd like to do some soaking experiments with a relatively large molecule. Can
someone suggest a program/method to display the solvent channels of a
crystal? We have the crystal structure. I'd like to see if the channels are
large
enough to allow the molecule to travel to the hypothesized
Hi,
I'm not aware of a program with an option to display channels in crystals but
if you use any of the currently available molecular display program and ask to
display symmetry-related molecules + adjacent unit cells, it should give you a
good enough idea of the spaces between molecules.
It is very hard to diagnose this sort of error - I didnt think
scalepack2mtz cared about data quality!
There is more likely some format problem.. Is a sca file meant to have some
sort of terminator?
But best to attach the offending sca file so that experts can check it..
Eleanor
On 26 June 2014
Just a remark: diffusion is a slow and random-walk process. Particularly
large molecules in viscous media (PEG anybody?) move (diffuse) slowly in
solution. To simply extrapolate from the fact that the ligand is smaller
than the solvent channels to the odds of the presence of a ligand is a risky
And yet halides--even iodide--permeate those same lysozyme crystals and
others entirely in 30--60 sec.
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard
Rupp
Sent: Friday, June 27, 2014 9:00 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject:
To get a rough idea of the solvent channels, one could use coot. By displaying
the symmetry molecules as Ca traces (an option hidden in the symmetry menu
under symmetry by molecule) one can set a large radius (100Å) and still
rotate the display. A more accurate display can be obtained by
For small ion soaking for phasing purposes, partial occupancy is not a
problem. For example, a few 1/2 occupied Iodines still can phase quite well.
1/2 a C is only 3 electrons, not that great. Add in higher displacement, and
odds are that the ligand interpretation will become difficult.
I recently reread an old science fiction book titled
Highways in Hiding by George O. Smith. To my surprise
there is some crystallography on page 58 (1967 Lancer book).
This is not exactly a great book and I am sure Joe Ferrara
would pan it.
It is available on Amazon and there are a number of
On 06/27/2014 06:33 AM, Bernhard Rupp wrote:
For small ion soaking for phasing purposes, partial occupancy is not a
problem. For example, a few 1/2 occupied Iodines still can phase quite
well.
1/2 a C is only 3 electrons, not that great. Add in higher
displacement, and
odds are that the ligand
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Protein Geometry Database Server V 1.0
http://pgd.science.oregonstate.edu/
Developed by Andy Karplus' laboratory at Oregon State University
We are pleased to announce the availability of an enhanced version
of the Protein
I have wanted for some time to search for catalytic-triad-like configurations
by defining three Ca-Cb bonds from known catalytic triads, then searching the
pdb for matches, but have not thought of a quick and/or easy way to do
this--can your software do this sort of thing, or is there some
You can use CAVER but you would have to make all the symmetry mates as one
chain in order to fool it. Still better to just do the experiment I think.
Either it will work or it won't, regardless of what any software tells you.
Just a wild idea : )
On Fri, Jun 27, 2014 at 5:06 PM, Yarrow Madrona
Hey Jeff,
Why not try the command line version of CAVER. It is easily adjustable and
provides nice figures of solvent accessibility for Pymol. It also prints
out a ton of stats in the log files if you want numbers.
-Yarrow
On Wed, Jun 25, 2014 at 1:10 PM, Jeff Holden hold...@uci.edu wrote:
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