Dear Peer and Eleanor,
This is indeed what I am suspecting: If the “twinning operator” in P32
puts 4 out of 5 protein chains on top of symmetry mates, is the “true”
space group then P32, with 5 twinned chains, or P3221 with 4 normal
chains and 1 chain on a special position? I would vote for the latter.
Best,
Herman
*Von:* CCP4 bulletin board <[email protected]> *Im Auftrag von
*Peer Mittl
*Gesendet:* Freitag, 27. August 2021 10:17
*An:* [email protected]
*Betreff:* Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
Dear Eleanor,
I indeed used r/tefmac for the refinement and it came up with the values
HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
refinement in P3221 would come up with the same occupancies for the
alternative conformations for the "extra" chain on the 2-fold axis. It
seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
sublattice with P3221 symmetry and it's just the "extra" chain, which
generates the twinning.
All the best,
Peer
On 26.08.2021 18:09, Eleanor Dodson wrote:
> Motto =mitti in predictive text!
>
> On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
> <[email protected] <mailto:[email protected]
<mailto:[email protected]%20%3cmailto:[email protected]>>>
wrote:
>
> Great, motto. I think you have nailed it! Did you use tefmac for
> twinned refinement? And if so what did it suggest the twin
> fraction is?
>
> On Thu, 26 Aug 2021 at 16:30, Peer Mittl <[email protected]
<mailto:[email protected]%0b>> <mailto:[email protected]
<mailto:[email protected]>>> wrote:
>
> Yes, the data indeed seems to be twinned and the tNCS has
> masked the twinning statistics, which is why I haven't
> considered it so far.
>
> I have not tried twinned refinement in C2 and P1 yet, but
> refining 4 chains in P32 with twinning yields a difference ED
> map that clearly indicates one (and just on!) orientation for
> the 5th chain. Thank you all for your suggestions.
>
> Have a nice evening,
> Peer
>
> -----"CCP4 bulletin board" <[email protected]
<mailto:[email protected]%0b>> <mailto:[email protected]
<mailto:[email protected]>>> schrieb: -----
> An: [email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
> Von: "Kay Diederichs"
> Gesendet von: "CCP4 bulletin board"
> Datum: 26.08.2021 16:41
> Betreff: Re: [ccp4bb] chain on 2-fold axis?
>
> Dear Peer,
>
> I suspect that the true spacegroup has lower symmetry than
> P3221, and that there may be twinning masked by tNCS.
> Subgroups of P3221 are C2 and P32 (
>
https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups
<https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups>
>
<https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups
<https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups>>
> )
> and of course P1.
> What I'd do is process the data, and solve (use the best chain
> of the refined P3221 model for MR) and refine the structure in
> these spacegroups.
> Inspect the results: If P1 is clearly better than P32 and C2,
> P1 is correct.
> If C2 (P32) is clearly better than P32 (C2), then P1 should
> give the same R-values as the better one; if so, P1 can be
> discarded.
> Try this with and without twin refinement - although it's hard
> to compare R-values of non-twinned and twinned refinements.
>
> The automatic way to do this is with Zanuda. If you run that
> locally, you can make refmac do twin refinement.
>
> For all resulting structures, I'd also feed the resulting
> Fcalc (!) into pointless. That should reveal that the packing
> is indeed close to P3221.
>
> Best wishes,
> Kay
>
>
> On Thu, 26 Aug 2021 11:54:06 +0200, Peer Mittl
> <[email protected] <mailto:[email protected]
<mailto:[email protected]%20%3cmailto:[email protected]>>> wrote:
>
> >Der CCP4 community,
> >
> >Is there a refinement program that can handle protein
> monomers sitting
> >on crystallographic 2-folds?
> >
> >This is probably a strange question but we have the following
> situation.
> >We have a 2.6 Ang datasets in SG P3221 (Rpim=4%, Isa=19.6)
> and a clear
> >molrep solution with 2 chains, albeit with tNCS (0/0/0.5)
> that can be
> >refined to around 27/33% Rfactor. According to Vm a third
> chain could be
> >present. So far so good, but there is clear difference ED for
> a third
> >chain sitting exactly on the 2-fold. Since the protein has a
> peculiar
> >shape, one can tell even its orientation. I can relax the
> symmetry to
> >P32 (or even P1) and place the missing chain with 50%
> occupancy on the
> >2-fold. This model can be refined, but I do not like this
> work around,
> >because the data is clearly P3221.
> >
> >Any hints on similar crystal pathologies and how they have
> been handled
> >would be helpful.
> >
> >All the best,
> >Peer
> >
>
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--
****************************
Peer Mittl, PD Dr.
Biochemisches Institut
Universität Zürich
Room 44M03
Winterthurer Strasse 190
CH-8057 Zürich
Tel. +41-(0)44-6356559
Mobile +41-(0)76-2776566
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