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Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
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Subject: Re: Electron density function for ligands in real space?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-10-29		Next message:
Subject: COOT 0.3.3 in OSX leopard does not work!!!
From: Azmiri Sultana azmiri {- dot -} sultana {- at -} GMAIL {- dot -} COM
Date: 2007-10-29


Subject: Re: Pseudo-merohedral twinning and Molecular replacement
From: Peter Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2007-10-29

Wilson plots are not very informative for the detection of twinning.

The spikes you see in your Wilson plots, could be due to ise ring
issues (both 3.89 and 2.24 A are at ice ring related d scapings.) The
very large mean intensity in those resolution shells could be due to
the fact that only strong reflections were not rejected during data
processing.
Since there is only 1 spike per dataset and the completeness in those
shells is not shown, one canot be sure I guess.

The NZ plots or L-stats could be useful.

Cheers

Peter










2007/10/29, Iain Kerr :
> Thanks very much for all the suggestions so far.
>
> While I am pursuing all the checks and balances for twinning here are
> the Wilson plots I forgot to attach before..I am not sure what is going
> on, especially in B !
>
> best,
> Iain
>
>
> >
> >
> > On Oct 25 2007, Iain Kerr wrote:
> >
> >> Dear all,
> >>
> >> I find myself posed with a rather interesting if somewhat confusing
> >> problem.
> >>
> >> Two crystals grown from the same conditions, let's call them A and B..
> >>
> >> A:
> >>
> >> Resolution 2.1A
> >> Spacegroup P4?
> >> Rmerge 0.137 (0.324)
> >> Mean((I)/sd(I)) 41.0 (17.8)
> >> Completeness 100 (100)
> >> Multiplicity 53.6 (56.3)
> >>
> >> 4/mmm is clear from indexing...systematic absences show a clear 4
> >> fold screw-axis..Pointless gives the most likely as P4_1 22 (I'm not
> >> clear on how it distinguishes P4_1 22 and P4_3 22..)
> >>
> >> Molecular replacement in Phaser, checking all the possible
> >> spacegroups, gives two outstanding solutions
> >>
> >> LLG Z-score
> >> P4_3 22 1972 41 (1mol/asu)
> >> P4_3 3801 54 (2mols/asu, ASU too full warning !)
> >>
> >> Solutions in other spacegroups had negative LLGs and/or were rejected
> >> for poor packing...the P1 solutions have LLGs of around -22000
> >>
> >> I rebuilt both solutions in ARP/wARP both giving Rfree ~32% and Rfac
> >> ~23%...rebuilding (most residues accounted for), adding ligands and
> >> water makes no difference.
> >>
> >> Different iterations of refinement/rebuilding eg. cutting resolution
> >> make no difference...the maps are really well defined and packing is
> >> very reasonable with no clashes in either spacegroup.
> >>
> >> B:
> >>
> >> Resolution 2.3A
> >> Spacegroup C222?
> >> Rmerge 0.187 (0.402)
> >> Mean((I)/sd(I)) 11.8 (4.8)
> >> Completeness 99.4 (98.8)
> >> Multiplicity 6.8 (6.6)
> >>
> >> Mosflm:
> >>
> >> 11 144 mC 255.61 64.32 63.97 90.0 90.3 76.1 C2
> >> 10 7 oC 90.69 90.74 124.09 90.3 90.7 89.7 C222,C2221
> >> 9 7 tP 63.97 64.32 124.09 90.7 90.3 90.0
> >> P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212
> >> 8 5 oP 63.97 64.32 124.09 90.7 90.3 90.0
> >> P222,P2221,P21212,P212121
> >> 7 5 mP 63.97 124.09 64.32 90.7 90.0 90.3 P2,P21
> >> 6 4 mC 90.69 90.74 124.09 89.7 90.7 90.3 C2
> >> 5 4 mC 90.69 90.74 124.09 90.3 90.7 89.7 C2
> >> 4 3 mP 64.32 63.97 124.09 90.3 90.7 90.0 P2,P21
> >> 3 1 mP 64.32 63.97 124.09 90.3 90.7 90.0 P2,P21
> >> 2 0 aP 63.97 64.32 124.09 89.3 89.7 90.0 P1
> >> 1 0 aP 63.97 64.32 124.09 90.7 90.3 90.0 P1
> >>
> >> This suggests pseudo-merohedral twinning to me...in C222/C222_1 ...a
> >> and b are almost equivalent, so the 4/mmm symmetry would be apparent ?
> >>
> >> The Rmerge in 422 (19.6%) is only slightly higher than C222/C222_1
> >> ....systematic absences again suggest a 4 fold...the curves
> >> calculated from the cumulative intensity distribution suggest partial
> >> twinning (when inputting C222_1 into the 'old' server to calculate a
> >> twin fraction from the partial twin test it says there are no twin
> >> laws for that spacegroup...)
> >> _
> >> The outstanding solutions in Phaser this time are:
> >>
> >> LLG Z-score
> >> P4_3 22 1317 35 (1mol/asu)
> >> C222_1 2237 46 (2mols/asu, ASU too full warning !)
> >>
> >> Rigid body refinement of the solutions give (C222_1 ) Rfree 43%, Rfac
> >> 42% and ( P4_3 22 ) Rfree 44%, Rfac 43%....I'm thinking this is high
> >> and the maps from Phaser although fitting the placed molecules have
> >> poor connectivity (high Rmerge anything to do with this ?)
> >>
> >> Going back to crystal A it turns out the same C222/C222_1 is found
> >> but lower down in the list amongst the other solutions...
> >>
> >> I have attached the Wilson plots for both crystals...A has a large
> >> spike at high resolution (which is why I cut the data to 2.4A to try
> >> and improve refinement, to no avail) and B looks horrid !
> >>
> >> OK, I think that is all the information I have at the moment...have I
> >> completely missed the correct symmetry..the Rmerge does seem high..
> >>
> >> I have not yet tried to detwin the data (if it truly is twinned) and
> >> perhaps that is impeding refinement ??
> >>
> >> Any suggestions would be greatly appreciated.
> >>
> >> Thank you,
> >> Iain
> >> _
> >>
> >>
> >>
> >
>
>
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