Dear Patrick,
I don't know how many comments you got offline, but here are my comments:
1) Ice rings. Even rings that are hardly visible by eye can disturb the data
such that Rfactors get stuck in the range you mention. Especially XDS, which is
otherwise an excellent data processing program,
There isnt much information here!
Funny that 3 chains are poor - does that mean one and a half heterodimers?
I presume you have checked spacegroup? Zanuda will test to see if any
higher symmetry is present..
Eleanor
On 29 April 2013 06:02, sonali dhindwal sonali11dhind...@yahoo.co.inwrote:
Dear Eleanor,
Thanks for the suggestion, I just checked on the Zanuda program, it is also
giving P1 as the best possible spacegroup for the molecule.
and by not refining well, I meant for the electron density which is broken at
many places at main chain, and poor electron density for the
herman.schreu...@sanofi.com wrote:
I would process or expand the data to P1, also expand your pdb file to P1 and
refine in P1 to see what happens. I would also run Phaser or some other
molecular replacement program on the P1 data to see what comes out.
process or expand? I don't understand
Hi Edward,
I and also others in the bulletin boards have had cases where the protein would
build e.g. tetramers with internal 222 symmetry, which would pack with the
2-folds parallel to the crystallographic 2-folds with say one 2-fold a little
shifted from the crystallographic position. In
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Ed,
just FYI: while this does not apply in the ccp4/mtz world, the fact
you might be missing is that in some refinement environments merging
is carried out by the refinement program so that the actual data can
be kept unmerged and e.g. the
FYI, I do know of one example of a solved structure where some of the
molecules in the ASU are poorly defined. In 1EKJ, 4 of the 8 molecules
in the ASU have low B-factors (mid 30s) and 4 have high B-factors
(50s-60s). In the unit cell these layers alternate. It is possible, if
everything else
You may also get some insights from TLS refinement.
Regards
Thierry
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger
Rowlett
Sent: Monday, April 29, 2013 12:27 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Poor electron density in some of the chains in an
Dear All,
Thanks for the help and suggestion
Francis, we used molrep for the structure solution. As I told that we already
have the structure of the same protein, but a variant. So, we used its single
chain (heteromer) as a model for molecular replacement.
and Eleanor, I deleted once that
On 04/29/13 12:26, Roger Rowlett wrote:
FYI, I do know of one example of a solved structure where some of the
molecules in the ASU are poorly defined. In 1EKJ, 4 of the 8 molecules
in the ASU have low B-factors (mid 30s) and 4 have high B-factors
(50s-60s). In the unit cell these layers
and 2VAK...average Bs for the twelve, sequence identical, chains vary from 28
to 53.
On 29 Apr 2013, at 22:09, David Schuller wrote:
On 04/29/13 12:26, Roger Rowlett wrote:
FYI, I do know of one example of a solved structure where some of the
molecules in the ASU are poorly defined. In
http://news.discovery.com/earth/rocks-fossils/sea-squirt-crystal-solved-130429.htm
Crystal Puzzle Solved with Sea Squirt
RE vaterite
Science 26 April 2013: 454-457.[DOI:10.1126/science.1232139]
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