Dear colleagues,
We deposited protein structures with modified lysine side chains and
were surprised that the PDB treats the modification as an independent
molecule, with a “LINK” record indicating the covalent bond – instead of
defining a modified residue (that’s what we had uploaded to the
Dear Ed,
What is the pH of your crystallization buffer? If it is acidic, either the
azide or the carboxylate may be protonated. Also the local environment of the
carboxylate can make a hugh difference in PKa. You could also use some Bayesian
logic: given the elongated linear density, what else
Dear CCP4BB,
The most likely components are those at the highest concentration in the
crystallization
or cryosolution.
And a few wild ideas to continue the discussion that is very important as
the ligands are
always very difficult to identify.
Example: If you have 1.5 M ammonium sulfate
Thanks all,
the pH is 6.7, azide is 3 mM, and there is no added ammonium.
I could get away with modeling as two waters since the separation is well above
the 2.2A that gets flagged as a clash in the PDB, still it's close enough
to suggest that two waters is not really what's there.
Enrico Stura
Dear Ed,
For me, 3 mM is a significant concentration. If you have another crystal left,
you could transfer it to a storage buffer without azide and collect a data set
and see if the density disappears. A very small molecule, non-covalently bound
on the outside of the protein should disappear
On Jul 7, 2013, at 1:44 PM, Ian Tickle ianj...@gmail.com wrote:
On 29 June 2013 01:13, Douglas Theobald dtheob...@brandeis.edu
wrote:
I admittedly don't understand TDS well. But I thought it was
generally assumed that TDS contributes rather little to the
conventional background
Dear all
I am working on a 30 kDa membrane protein which forms a functional dimer. The
protein is His-tagged at N-terminal. In small scale expression screening from
whole cells, there is only a single band on Western blot at 30 kDa. But, after
purification, additional bands appear at 60 and
Hi everyone,
I just wanted to ask if there is a professional association for
crystallographers in the US. When I googled it I came across The American
Crystallographic Association. Is that the only one?
Thank you,
Maher
