Dear Vaheh,
I agree with you, at least in your last statement. I guess we all agree that
certain molecules can occupy special positions on true rotation axis. Strictly,
this is only possible if the molecule obeys the rotation symmetry. For water
molecules on 2-folds you already have to make assumptions about the "invisible"
protons. I guess, many of us have seen even larger and asymmetric solvent
molecules, such as glycerol, MPD or buffer molecules on special positions,
which locally break the crystal symmetry. The work around for this issue would
be to define two alternative conformations for this molecule, because these
conformations do not "see" each other, as pointed out by Herman. But where is
the upper limit for the molecular weight of this molecule?
I (and perhaps most other crystallographers) would not refine such a case as a
twinned structure in a lower symmetry space group, because the major part of
the AU obeys the crystal symmetry. Furthermore, there is a fundamental
difference between crystallographic symmetry and the symmetry of a twin law.
The crystallographic symmetry covers the entire crystal, whereas the twin law
just relates twin domains locally. Refining a true P3221 structure as a twinned
P32 structure is simply the wrong thing to do.
All the best,
Peer
-----"CCP4 bulletin board" <CCP4BB@JISCMAIL.AC.UK> schrieb: -----
An: CCP4BB@JISCMAIL.AC.UK
Von: "Oganesyan, Vaheh"
Gesendet von: "CCP4 bulletin board"
Datum: 27.08.2021 13:56
Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
How P3221 can be an option if it assumes chain on axis? I guess I’m missing
something, but per my belief only those sg will be possible for which there is
no axis going through the extra molecule. P1 sg looks the only correct option
here in my humble opinion.
Democracy (voting) depends on science. However, the reverse is not,
thankfully.
Vaheh
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Peer Mittl
Sent: Friday, August 27, 2021 6:32 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
Dear Herman,
The answer probably depends on the impact of the "extra" chain on the
sublattice. If there is no impact the "true" space group is P3221 with
one chain on the special position. If the swapping of the extra chain
influences the sublattice P32 (or C2 or P1, as pointed out by Kay)
twinned to P3221 might be the better description.
All the best,
Peer
On 27.08.2021 10:56, Schreuder, Herman /DE wrote:
>
> 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 <CCP4BB@JISCMAIL.AC.UK> *Im Auftrag von
> *Peer Mittl
> *Gesendet:* Freitag, 27. August 2021 10:17
> *An:* CCP4BB@JISCMAIL.AC.UK
> *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
> > <eleanor.dod...@york.ac.uk <mailto:eleanor.dod...@york.ac.uk
> <mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk>>>
> 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 <mi...@bioc.uzh.ch
> <mailto:mi...@bioc.uzh.ch%0b>> <mailto:mi...@bioc.uzh.ch
> <mailto:mi...@bioc.uzh.ch>>> 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" <CCP4BB@JISCMAIL.AC.UK
> <mailto:CCP4BB@JISCMAIL.AC.UK%0b>> <mailto:CCP4BB@JISCMAIL.AC.UK
> <mailto:CCP4BB@JISCMAIL.AC.UK>>> schrieb: -----
> > An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> <mailto:CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>>
> > 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
> > <mi...@bioc.uzh.ch <mailto:mi...@bioc.uzh.ch
> <mailto:mi...@bioc.uzh.ch%20%3cmailto:mi...@bioc.uzh.ch>>> 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
> Fax. +41-(0)44-6356805
> Mail mi...@bioc.uzh.ch <mailto:mi...@bioc.uzh.ch>
>
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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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Mail mi...@bioc.uzh.ch
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