Dear Eleanor,
many thanks for all your help and suggestions. We finally have solved
the mutant structure. The trick was to use the pseudo translation (there
was not any 2 fold axis in the self rotation) with MOLREP which found
two molecules and then applied the pseudo translation to provide us with
the other two molecules yielding a tetramer. I think that initially the
programs and also ourselves missed the pseudo translation because it
is very close to the crystallographic one (0.49 0 0.48). Many thanks
to Peter Zwart who also advised us to follow the same procedure.
Demetres
Eleanor Dodson wrote:
Oh dear - this is tricky!
You could have a dimer in the asymmetric unit, or two monomers in the
asymm unit which generate dimers using the crystallographic 2 folds.
Things worth checking -
What does the self rotation show? Is there a clear 2 fold axis which
is different from the crystallographic one?
If so you can use all of MOLREPs cleverness to use the self rotation
definition and the pseudo translation.
(Under search parameters you can give the self rotation list of
solutions - just use self rotation with 1 or 2 solutions and edit out
the top one which will be the crystallographic 2 fold)
It will find the pseudo trans vector automatically.
If the only 2 fold is the cryst one then you need to search for 2
molecules with the pseudo translation.
Eleanor
What is the solvent content of the native - the mutant has a smaller
volume so less solvent - is that feasible?
I think I would generate P1 data Demetres D. Leonidas wrote:
Dear Eleanor,
Yes the native is a dimer and we did the search using the dimer as a
model but we had similar results (i.e. all programs find one
molecule). The graphs from TRUNCATE show rather "normal" and I am
attaching a gif file with the plot for the cumulative intensity.
As for pseudo-translation running the "Analyse Data for MR" option in
ccp4 in the patterson map we are getting a significant peak at
fractional coordinates 0.4897 0.0 0.4767. How this can help ? Do we
need to apply this pseudo translation to the solution we are getting
from molrep ?
many thanks
Demetres
P.S. I will summarize for the members of the list all the suggestions
I will get at the end
Eleanor Dodson wrote:
You dont say whether the molecules in the native cell form a dimer -
if so I would search with that (you may need to turn off the packing
search)
Or whether there is a pseudo translation vector in the mutant form..
Or what the data analysis graphs from TRUNCATE show - are they
"normal"?
Eleanor
Demetres D. Leonidas wrote:
Dear all,
we have encountered a problem in solving one mutant structure. The
mutant protein crystallizes in the same space group as the native
(C2) but the unit cell dimensions are different. These for the
native structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant
160.4 32.3 107.0 90 125.7 90. As a result the mutant structure has
four molecules in the asymmetric unit while the native had two.
When we run molecular replacement all programs (CNS, molrep, and
amore) find only two molecules. Phaser finds four but when we try
to refine the Rfree does not drop below 0.44 if we use four
molecules and 0.53 if we only use two no matter how well we built
the molecule and regardless of any addition of water molecules (the
resolution of the data is 2.1). The interesting thing is that in
the electron density map we can clearly see density for a substrate
analog that was included in the crystallization media. Do you
thing that we have a case of twinning here ? We have to mention
that Tod Yates served did not indicate any perfect merohedral
twinning (partial merohedral twinning for this space group is not
possible).
We would appreciate any comments
Many thanks
Demetres
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--
Demetres D. Leonidas, Ph.D.
Structural Biology & Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
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Tel. +30 210 7273841 (office)
+30 210 7273895 (lab)
Fax. +30 210 7273831
E-mail: [EMAIL PROTECTED]
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