[phenixbb] P3 pseudotranslation

Ethayathulla A.S ethayathulla at gmail.com
Sun Jan 13 21:07:43 PST 2013


I am trying to solve a structure with P3 Pseudotranslation at 3.5A. The 3.5
dataset have cell of 150,150,200 and 5A dataset have smaller cell 150,150,
100. The data can be scaled in P321, p3221,p3121 with similar rsym (6
(54).  Pointless gave me Spacegroups as P3221 or P3121 as soln. I tried
Phenix.xtriage it showed me 40% Pseudotranslation peak ( 0,0,0.5) for 3.5A
dataset as the c-axis is double that of 5A data. According to cell content
analysis it can be dimer in 3.5A and monomer for 5A dataset. So I tried MR
with both datasets with homology model build using similar fold protein. I
got solns for dimer with LLGs with 1000's in P3221,P3121,P321 with 3.5A
dataset. There were 28 solutions


    SOLU SET  RFZ=2.0 TFZ=8.2 PAK=0 LLG=259 TFZ==11.3 LLG=1181 TFZ==28.4 (
 SOLU SPAC P 32 2 1)

   SOLU 6DIM ENSE partial EULER 94.4 2.7 25.5 FRAC -0.07 -1.07 -0.81 BFAC

   Solution #2 annotation (history):

   SOLU SET  RFZ=2.0 TFZ=8.2 PAK=0 LLG=225 LLG=1066 (   SOLU SPAC P 31 2 1)


So I refined the solns. of P3221, p321 it refined to 44/54 after that it
doesn’t go down. The 0.5 Pseudotranslated molecule can been as symmetry
molecule along c-axis. The packing looks very good. I have attached the
image of it with native patt map. I deleted one monomer and refined to
check the solution I could see clearly see the other molecule.  I could see
2n+1 odd reflections to be weak.

To check whether two fold can be due to twinning due to pseudotranslation I
could not observe it. So I tried to see check whether the it can be P32
merohedral twinning with pseudotranslation with  twinning of 0.36
(h,-h-k,-l) from yeates server. I try to use the dimer of P3212 and try for
alternative spacegroup which yield me unique soln in P32. I refined the
molecule four molecule which yielded me 46/49 and when I apply twinning
fraction the r-factor decreases to 40/45.

Similarly for 4.5A dataset I used dimer of 3.4 dataset dimer which yield me
solution in P32 but cannot refine it gets struck for 45/50.I tried to use
the dimer with 5A dataset I get unique solu and refine with merohedral
twinning the r/freeR goes to 38/57.

How I can check whether it is P32 merohedral twinning with Pseudotranslated
or P3221. Also the patterson analysis another peak of height 4% ( 0.050,
0.102, 0.495 ) :    4.452 . Is it significant ?

Any suggestion will be helpful

Thank you



 Patterson analyses from phenix.xtriage

 Frac. coord.        :    0.000    0.000    0.500

 Distance to origin  :  103.157

 Height (origin=100) :   40.427

 p_value(height)     :    2.740e-04

The full list of Patterson peaks is:

  x      y      z            height   p-value(height)

( 0.000, 0.000, 0.500 ) :   40.427   (2.740e-04)

( 0.050, 0.102, 0.495 ) :    4.452   (9.782e-01)


Dr. A.S. Ethayathulla
Dept of biophysics
AIIMS, new delhi
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