Hi Derek,
The assymertic unit of the self rotation function is only one
hemisphere, for example the north hemisphere.
So, if you look on the kappa = 180 °, horizontally in the equator you
have the crystallographic axis and 2 perpendicular 2-fold axis on to the
other, the one in the near middle is nearly but not really parallel to
c*, but sure you will have the symmetric of this 2-fold axis by the
crystallogrpahic axis, which is in the list but NOT represented in the
stereogramm ...
Ok, hope this is not to confusing .... and that it helps ...
cheers
claudine
Derek Logan wrote:
Hi everyone,
Can anyone help me with interpretation of a self rotation function
and native Patterson from a dataset with pseudosymmetry? I've always
been a bit poor on spherical polars. The space group is P21 with beta
= 92.2°. The kappa=180° section of the SRF, calculated using Molrep,
is at
http://mole.mbfys.lu.se/~derek/selfRF_180.png
and contains two big peaks around 7 sigma. I'm having trouble
identifying these in the list of peaks from Molrep:
theta phi chi alpha beta gamma
Isym_i Isym_j
Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 1 1
Sol_RF 1 90.00 -90.00 180.00 0.00 180.00 0.00 1 2
Sol_RF 1 90.00 90.00 180.00 0.00 180.00 0.00 2 1
Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 2 2
Sol_RF 2 158.56 180.00 180.00 0.00 42.89 -180.00 1 1
Sol_RF 2 111.44 0.00 180.00 -180.00 137.11 0.00 1 2
Sol_RF 2 111.44 0.00 180.00 180.00 137.11 0.00 2 1
Sol_RF 2 21.44 0.00 180.00 180.00 -42.89 0.00 2 2
Sol_RF 3 165.65 0.00 180.00 -180.00 28.70 0.00 1 1
Sol_RF 3 104.35 -180.00 180.00 0.00 151.30 180.00 1 2
Sol_RF 3 104.35 180.00 180.00 0.00 151.30 -180.00 2 1
Sol_RF 3 14.35 -180.00 180.00 0.00 -28.70 180.00 2 2
It seems to me to be two copies of peak 2. I believe theta starts in
the middle, perpendicular to the page and phi starts on the x axis,
thus the peak just below the centre would be (21.44, 0, 180). I
presume that the second peak is the symmetry-related (158.56, 180,
0)? However where is (111.44 0 180)? I would expect to see this near
the bottom of the plot, but it's not there. I'm sure I'm missing
something fundamental about the symmetry of the SRF projection, but
unfortunately I don't have a supervisor to bug about this (I *am* the
supervisor...)
In the native Patterson
http://mole.mbfys.lu.se/~derek/nativePatterson.png
there are two peaks of almost equal height. How can this be
reconciled with having only one strong peak in the SRF? There are
most likely two dimers in the asymmetric unit, but there may only be
one, with very high resulting solvent content. What's more the
molecules are leucine- rich repeat proteins and have weak internal
symmetry. I believe this was an issue with the ribonuclease
inhibitor, but looking briefly at the crystallisation article and
structure article I wasn't able to find a rationalisation of this
problem. The 2-fold is perpendicular to b*. How could this cause the
two peaks?
Thanks
Derek
--
*************************************************************************
Dr Claudine MAYER
MCF Université Paris 6
LRMA Equipe 12 UMR S 872
Laboratoire de Bactériologie (5ème étage gauche)
Faculté de Médecine PITIE-SALPETRIERE
91 bd de l'Hopital
75634 PARIS Cedex 13
tel : 01 40 77 95 56
fax : 01 45 82 75 77
mobil: 06 07 23 51 16
[EMAIL PROTECTED]
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