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]>> 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]>> 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]>> schrieb: -----
An: [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>
)
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]>> 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
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