[ccp4bb] Pseudo Merohedral twining in C2 space group?

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CCP4bb <-- 2007 <-- December 2007 <-- 08 December 2007

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Subject: ncs phased refinement
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2007-12-07

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Subject: Re: ncs phased refinement
From: "Winn, MD (Martyn)" m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-12-08

Subject: Pseudo Merohedral twining in C2 space group?
From: Xiaolei MA xiaolei {- dot -} ma {- at -} GMAIL {- dot -} COM
Date: 2007-12-08

Dear ccp4bb community:

Recently I have collected a se-met SAD dataset from a protein crystal that
diffracted to better than 2.4A. The dataset can be ambiguously processed in
the following space groups:

I222: 68.938, 99.376, 115.690; with 4 monomers/A.U. 66% solvent content,
Rmerge=0.104
C2: 152.366, 68.907, 99.365; beta 130.605; with 8 monomers/A.U. 66% solvent
content, Rmerge=0.077

SOLVE readily identified 3 Se atoms in I212121 (7 in C2) space group and
RESOLVE gave me a partial models which were completed afterwards. However
the refinements were problematic as indicated by high R/Rfree around 42%/45%
in both I212121 and C2. Moreover, high B factors and extremely poor main
chain density were observed for 2 monomers out of 4 monomers in I212121, or
4 monomers out of 8 monomers in C2 space group.

The output from "truncate" in both space groups showed a big discrepancy in
the cumulative intensity distribution for acentric reflections (Fig 1). In
addition the merohedral twin detector by Padilla-Yeates Algorithm indicated
the presence of twinning as well (Fig 2). However the 4th moment of E (the
ratio of the average squared intensity to the square of the average
intensities, /^2=3.1627) is around 3 (Expected value=2, Perfect
Twin=1.5); the acentric /E^2-1/ value is 1.053, which is even higher than
the theoretical value of 0.736. I assume the above two observations are due
to the presence of the high degree of NCS and pseudo-translation:
(pseudo-translation is detected by sfcheck (%): 25.2,
pseudo-trans.vector/frac/:
0.463 0.000 0.000) Is my understanding correct?

As merohedral twinning is not possible in either I212121 or C2, I have been
investigating pseudo merohedral twining in C2. The matrix (matrix A) used to
transform C2 to I222 was obtained by XPREP: [0 1 0, 0 0 -1, -1 0 -1]. The
twin operator was obtained by multiplying the inverse of A, two fold axis
[-1 0 0, 0 1 0, 0 0 -1], and A three matrix one after another: [-1 0 -2, 0
-1 0, 0 0 1], which is equal to (-h-2l, -k, l). The twin operator (TWIN) and
an arbitrary twin fraction (BASF) from 0.1-0.5 was input into shelxl for
twinning refinement. The twin fraction was invariablely refined to ~0.47
regardless of the starting value. The R/Rfree also decreased to 32%/34%
after coordinate and B factor refinement. The electron density looks mostly
continuous for main chain, although the density for some side chains is
still ugly.

This is the first time I encountered any kind of twinning problem in my
research, the R/Rfree is still way too high for a 2.4A structure and I am
having a tough time in getting them down at the moment. Can anyone give me
any advice on my handling of these data? Any suggestions will be highly
appreciated.

--
Mr. Xiaolei MA (Charlie MA)
Ph.D. Candidate
Department of Biochemistry
School of Medicine
Case Western Reserve University
10900 Euclid Avenue
Cleveland, OH 44106-4935
Phone:
216-313-3867(cell)
216-368-6833(office)

"All human wisdom is contained in two words; wait and hope" Alexandre
Dumas

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CCP4bb <-- 2007 <-- December 2007 <-- 08 December 2007

Previous message:
Subject: ncs phased refinement
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2007-12-07 Next message:
Subject: Re: ncs phased refinement
From: "Winn, MD (Martyn)" m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-12-08