Hi Demetres,
not sure if this is going to be usefull, but here I go.
Your native has a twin law that and your cell is pseudo C222. The
mutant is not. pseudo merohedral twinning is not handled well by the
twin server you derscribe as it relies on lookup tables.
There is no obvious 'perfect' relation between two unit cells. The
ratio between the two unit cell volumes is about 1.8 and a sublattice
of your native cell that comes close to the lattice of your mutant
does exist. iotbx.explore_metric_symmetry tries to find you possible
relations. It uses niggli settings though and the output is not very
user (or even developer) friendly:
--------------------------------------------------------------
Mutant niggli cell : 32.3 81.8 90.1 76.8 79.7 78.6
Native niggli cell : 33.1 53.2 73.4 90.3 90.0 108.1
/ 1 0 0 \
matrix : M = | 0 2 1 |
\ 0 0 1 /
(matrix M acts on the real space basis vectors of the Native niggli cell)
Additional Niggli transform: x-y,-y-z,y
Additional similarity transform: x,y,z
Resulting unit cell : 33.1 90.5 90.9 67.8 79.5 79.5
Deviations : -2.5 -10.6 -0.8 8.9 0.2 -0.8
Deviations for unit cell lengths are listed in %.
Angular deviations are listed in degrees.
--------------------------------------------------------------
Details of what the matrix M means is found in
http://www.ccp4.ac.uk/newsletters/newsletter44/articles/explore_metric_symmetry.html
It is too early for me to understand if the pseudo translation you see
at (1/2,0,1/2) is related to the transfomration shown above, but if
you multiply this translation in C2, you do end up with a smaller unit
cell. why don't you try this:
run xtriage (a latest version) on your mutant data and see what the
patterson analyses tells you what it thinks the unit cell is if the
patterson peak were a true crystallographic operator.
Take that unit cell and compare it to your native
(iotbx.explore_metric_symmetry might be usefull).
Again, I am not sure that a relation is there, but if it is real, you
can get the coordinates for your mutant structure almost directly from
your native structure.
The relations one sees can be deceiving though, it could be
crystallographic numerology.
Cheers
Peter
2007/7/13, Demetres D. Leonidas <[EMAIL PROTECTED]>:
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
--
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)
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Fax. +30 210 7273831
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