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
>> _
>>
>>
>>
>
|