Hi,
Does anyone have experience with molecular replacement at low
resolution? I have a 6Å dataset with probably 3-4 monomers per ASU.
Phaser doesn't seem to give me clear results. Can I get some advice?
Any comment will be appreciated.
Thanks a lot,
Junyu
===
NCS.
Good luck,
Pete
-Original Message-
From: CCP4 bulletin board on behalf of Anjali Mehta
Sent: Thu 3/6/2008 7:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Molecular replacement of a multidomain protein
Dear All,
I am working with a Bifunctional protein of molecular weight ~60 kD
EPMR (now Open-EPMR, http://www.epmr.info) is an excellent alternative
for finding difficult, high-dimensional MR solutions. Experiment with
various resolution limits. We solved an asymmetric unit with 3
difficult-to-place dimers of low sequence homology by gradually
increasing the high-resolut
I've had a very good experience with MrBump:
http://www.ccp4.ac.uk/MrBUMP/
Not only because of the program itself, which was able
to find an unexpected template for the problematic
chain (the first one was straightforward in Phaser),
but also because of great support from Martyn & Ron.
It's defin
Dear All,
I am working with a Bifunctional protein of molecular weight ~60 kDa.
I have a 3.3 angstrom native dataset. The matthews number show there are 6
molecules in the asymmetric unit.
The structures of the individual domains are already known from prokaryotes.
The sequence identity with the k
The answer to your question is called Phaser. Using Phaser, you can input
multiple search models in one search routine to look for
solutions.
You should read the online manual and tutorials, if you are not already
familiar with Phaser. You can also 'modify' or appropriately
'trim' your search
Dear All,
I wanted to solve one of my new structures by molecular
replacement. I got three short search motifs from three
different structures available in the PDB. My question is, how
do I use all the search models to solve the structure.
With by best regards,
Sekar
(\_/)
(='.'=)
(
Dear All,
The authors of the following paper used molecular replacement of the
substructure to locate the heavy atoms. The known 11-fold symmetry meant that
the heavy atoms had to be in a circle - molecular replacement with circles of
different radii did the trick.
Antson et al. Nature, Vol
Many times when we search for anomalous scatterers, we have some a priori
info about their relative positions. For example, many proteins have
sequence-adjacent methionines, which tether the anomalous scattering
positions to certain distances. Again, there are many heavy atom derivatives
which have
You dont say how close your sequence ID is for your new protein and the
model. It is often very hard to kick start refinement with low homology
And what about internal symmetry
Is there a Non crystallographic translation?
Does the self rotation function show a relationship between the two
mole
CCP4 bulletin board wrote on 05/10/2007 09:31:59
PM:
> Hello,
> I'm an undergraduate and recently crystallized and obtained 2.9A
> diffraction data for a protein which is predicted to fold into a WD40
> 7-bladed beta-propeller structure (which has been crudely verified by
> cryo-EM by another lab
Hello Scott,
hmmm - it is quite difficult to do a good analysis of your problem,
remotely. You've tried the enantiomorphic space group I4(3), just to be
sure? In principle, the molecular replacement solution given by Phaser
sounds good, but this is no proof of whether it's correct. What sounds
Hello,
I'm an undergraduate and recently crystallized and obtained 2.9A
diffraction data for a protein which is predicted to fold into a WD40
7-bladed beta-propeller structure (which has been crudely verified by
cryo-EM by another lab). The space group appears to be I4(1) with
unit cell pa
Hi, Dear all,
Firstly ,I'd like to thank all the people for their kind help,
especially Miguel, Bernie ,Mark, Moody, Eleanor, Eaton , Peter and
lots of others Without your help, I wouldn't make it this far.
Secondly, I'd like to share some of the experiences. We had a hard
time trying to do
101 - 114 of 114 matches
Mail list logo
