Re: [ccp4bb] molecular replacement and twinning problems

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: molecular replacement and twinning problems
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2009-04-28

Next message:
Subject: ccp4mg and OS X
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2009-04-28

Subject: Re: molecular replacement and twinning problems
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-04-28

You dont mention any twinning tests?
The L test, now part of the newest ctruncate is pretty good at detecting
twinning even with the NCS translation.
And SFCHECK does a good job too.
If these are inconclusive I would not assume twinning.

Usually you can get solutions for MR with twinned data, but I havent
much experience of the signal quality..
Can you solve it in P1 then sort out the spacegroup later?
Eleanor

Kay Diederichs wrote:
> Dear all,
>
> we have crystals that nicely diffract to 1.7 A (sharp spots), with the
> following characteristics and findings:
> a) the data appear as P212121, with axes 117.2 133.6 138.3 (if
> reduced in P1, the largest deviation of any angle from 90° is 0.2°);
> the odd screw-axis reflections are mostly indistinguishable from
> noise; the data do not scale significantly better in P2/P21 (any
> setting) or P1.
> b) there is a good model available, with coords known from a complex
> of this protein with another one; two molecules of this model would
> give 64% solvent in P212121 which appears reasonable for a membrane
> protein
> c) the structure cannot be solved with this model in P212121, nor can
> it be solved in P222, P2122, P2212, P2221, P21212, P22121, P21221
> d) we conclude that the true space group must be P2 or P21 (with one
> of the three possible settings), with almost-perfect twinning. Or it
> is P1 with tetartohedral twinning. There are thus still six + one
> possibilities.
> e) MOLREP tells us
> --- Check Patterson for pseudo-translation ---
> PST_limit : 0.125 of origin peak
> INFO: pseudo-translation was detected.
> Origin Patterson peak: P,P/sig : 57.748 257.690
> 1 Patterson. peak : p,P/sig : 28.773 128.395
> 2 Patterson peak : P,P/sig : 16.551 73.856
> 3 Patterson peak : P,P/sig : 8.502 37.936
> Peak 1: trans.vector /ort/ : 0.011 55.688 69.399
> trans.vector /frac/: 0.000 0.416 0.500
> Peak 2: trans.vector /ort/ : 58.554 66.863 0.000
> trans.vector /frac/: 0.500 0.500 0.000
> Peak 3: trans.vector /ort/ : 58.565 11.385 69.399
> trans.vector /frac/: 0.500 0.085 0.500
> INFO: translation vector of peak 1 will be used.
>
> Two molecules (for the orthorhombic spacegroups) may produce only one
> pseudo-translation vector. As there is more than one strong
> pseudo-translation vector, I conclude that we have at least 3
> molecules in the ASU (consistent with monoclinic).
>
> f) we've calculated all seven molecular replacement searches of d) in
> MOLREP. The contrast is very high in all cases. However, Refmac
> rigid-body refinement of the solutions, with "Twin refinement"
> activated, gives about 51% R and the same for Rfree (give or take 1
> %), in all cases.
>
> I'm wondering: how reliable is a rotation search in the presence of
> perfect twinning? Is there any molecular replacement program that can
> take a given twinning operator into account in the rotation and
> translation search?
>
> Any other hints what to try?
>
> best,
>
> Kay

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: molecular replacement and twinning problems
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2009-04-28

Next message:
Subject: ccp4mg and OS X
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2009-04-28