Dear Vineet
Following points shall be kept in mind.
1.If you have been able to model most of the protein
into the electron density, then its a bit strange.
your refinement parameters suggest that refinement is
still away from convergence.
2.You might be trapped in local minima, and in this
case
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School of Biological Sciences
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crys
In Coot (0.3.2 and later) you could also try the following:
- center on the serine to be phosphorylated
- click Extensions->Phosphorylate this residue
and Coot will sort out phosphorylation, renumbering etc in no time.
JED
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PR
I wonder if anyone would care to share experiences/ideas/biases that
relate to the use of mass spectrometry to verify the identity of
protein constructs used for crystallization. Our experience with
different MS facilities has been checquered.
Specifically:
What's the current thinking on
I second Dr. Loll's question, and would like to be CC'd in whatever MS tips,
including
service-providers, are sent. I have been having a bit of a debacle with a
certain MS service provider.
Jacob Keller
==Original message text===
On Wed, 05 Sep 2007 11:41:52 am CDT Patri
Hi,
Thanks for the reply to my earlier query.
I am looking for the coordinates of few organophosphates which can bond
covalently to protein as follows .
1) Para-oxon: O,O-Diethyl-O-para-nitrophenyl phosphate
2) Sarin: 2-(fluoro-methyl-phosphoryl)oxypropane
3) Soman: 3-(fluoro-methyl-phosphoryl)o
Hi Sam:
You can define a SMILES string, put that in coot, and it will create
coordinates.
Similarly, within phenix, you can do this with elbow.builder and then optimize
is either with built-in forcefields or with an external QM program. It will
give you a reasonable (usually) cif file that you
If you have a very pure protein sample, you'll want to use an ESI-ion trap
for analyzing proteins of that size. It should be possible to get an exact
mass (i.e. within a single Da). It's possible, but very rare, to get exact
masses of proteins up to 100 kDa using ESI-ion trap instruments.
If you
... all these are correct indeed - but ESI-TOF is also a nice
solution, especially coupled to an LC system.
My understanding was that MALDI-TOF is better for smaller fragments,
accuracy can be about 10 Dalton ...
for more info there is a useful short review of the use of ms
techniques for s
Hiya
For verification purposes we almost always N-terminal sequence (we are
fortunate in that we have such a facility on site so that the samples can be
turned round fast) - old technology but good and solid! We then usually
combine these data with a Mass Spectra (MALDI-ToF-Tof - on site - is
Hello,
While I am not a professional MS person, I have had the privilege of working
with many MS scientists and some knowledge has rubbed off despite my best
efforts to stay benighted. All the correct information in the post below is
therefore credited to the MS community whereas all the errors
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