We have been solving a protein complex at 3.1 A by molecular replacement. One
copy of two chains in the asymmetric unit.
The two chains have fairly different average B factors. As would be expected isotropic B factors in refmac overfits the
data and leaves a large gap between R and Rfree. TLS
Dear All,
last Friday I posted the following question:
I have a heterodimer of two related subunits (A and B). Now I
want to superimpose it using a secondary structure matching
(SSM) algorithm (e.g. CCP4 superpose or the coot algorithm)
such that the superposition matches A onto B and B
Norbert,
Sorry for this late reply. SSM will find multiple alternative matches
but most implementations just show you the 'best'. The Superposition
tool in CCP4mg uses ssm and has an option to look through the non-
optimal matches - hopefully one of these will be the one that you want.
Applications are invited for a Wellcome Trust funded position to
investigate the structure, assembly and functioning of nuclear
receptor co-regulator complexes. The appointee will join the research
group of Professor John Schwabe working in the newly-appointed Henry
Wellcome Laboratories
Nick,
there was a discussion of this three weeks ago. Check this thread
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg14133.html
I still maintain the view that appropriately tight restraints are the
way to go and not the grouped B-factor refinement (at least not the way
it is currently
Dear All,
this is an announcement of the EMBO Practical Course on Solution Scattering
from Biological Macromolecules. The message is sent to several listservers,
and we apologize if some of you will receive it more than once.
With best regards
D. Svergun,
M. Roessle,
M. Petoukhov,
P. Konarev,
Dear colleagues:
I am trying to interpret the results of the substitution of a Methionine
with Alanine. Following is the kinetic data on the mutation -
1. Km increased by 0.5 fold
2. Vmax decreased by 3.5 fold
3. Kcat decreased by 4 fold
4. Kcat/Km decreased by 10 fold.
5. Activity at saturating
Dear Crystallographers,
Having looked into the structure I mentioned using the atomic contacts
feature of the whatif server, it seems that both the 1.0 Ang structure I
previously mentioned, as well as another, lower-resolution related
structure, have a significant number of waters which are
Dear Micheal and Matthew:
Thank you for your inputs on the structure-function analysis data.
As pointed out by Micheal - the change in Km (For Met to Ala mutation)
is not much. Could this be intepreted simply that the mutation does not
change the affinity of the enzyme for the substrate because a
