Hi,
If you search with a dimer, then the version of Phaser in CCP4 doesn't know
that there is internal symmetry in your model, and it will find two
solutions that are equivalent by the internal symmetry, but would not be
equivalent if the model were not symmetric. The latest version of Phaser
(which is available in Phenix, and should be in the next CCP4 release)
identifies internal symmetry and would recognise the two solutions as being
equivalent.
You can check this by reading the two solutions into coot, using ssm
superpose to superimpose the first monomer of the first solution on the
second monomer of the second solution, and seeing whether the
transformation is some combination of crystallographic symmetry and an
allowed origin shift.
Best wishes,
Randy Read
On Oct 21 2009, X Xiong, Cellular & Molecular Medicine wrote:
>Hi All,
>
> Thanks for all the replies, I would like to add more information, after
> reindex it to P21212, the cell parameter is a=88.71, b=116.26, c=55.12,
> the molecule is a long rod like head to head dimer with a length of 110Å
> (55Å long for each monomer) and we used the dimer to search the
> orthorhombic data, two solutions were found as shown in the original
> thread which can be both refined to almost the same very good R/Rfree,
> coot was used to generated the symmetry related molecules from both
> solutions and the two solutions had the same packing but translated along
> the b axis by 31.9Å, thus clashed into each other and made a mess in the
> overlap region, so I think they are not crystallographically the same
> solutions, unless the origin of the cell in P21212 can be placed on
> b-axis arbitrarily, and I think Phaser will also prune the
> crystallographically same solutions.
>
> Interestingly, the most prominent pseudo-translational peak (1/3 of the
> origin peak), has a fractional vector 0.5000 0.2741 0.5000, and the
> fraction on b axis = 0.2741*116.26 = 31.8755Å, and that is exactly how
> long the two solutions translated along the b-axis, I don't know what
> that means, does these information verify this is the second case Eleanor
> suggested? if so should I keep the messy overlapped region and set the
> rest 0 occupancy to check the density?
>
>Thanks for all the suggestions so far!
>
>Xiaoli
>
>
>> From the Pattersn peak it seems very likely that you have two molecules
>> in the asymmetric unit seperated by the very vector that seperates your
>> two MR solutions, and both MR solutions are correct?
>>
>> Or is that not possible? Is there no room for 2 molecules in the
>> asymmetric unit, and the Patterson peak isa function of the "highly
>> repetitive dimer" Eleanor If that is so you need to set the occupancy of
>> any differences in the solution to 0.00 and check from the maps after
>> refinement if you can see which copy of the molecule fits the difference
>> density best - it would nice if you had a TRP/ALA pair of residues or
>> something very distinctive.. Eleanor
>
>
>X Xiong, Cellular & Molecular Medicine wrote:
>> Dear Crystallographers,
>>
>> We got a highly repetitive dimeric protein solved by SeMet-SAD in P21
>> crystal form, and I am now trying to solve a dataset collected from a
>> non-reproducible orthorhombic crystal of the same protein using the
>> structure refined from P21 data.
>>
>>> From the Scala statistics, the orthorhombic crystal diffracted to
>>> 2.2Å with
>> an I/sigma of 3.1 at outmost shell; 98% complete overall, 89% complete
>> 43.4-7.0Å, 99% complete 2.32-2.2Å, no twinning was detected. Due to
>> the incompleteness at low resolution, it was hard to determine which
>> orthorhombic space group it is in so data was scaled in P222. Very
>> strong pseudo-translational symmetry has been detected by
>> self-Patterson, as shown for reindexed data P21212 (space group later
>> found by Phaser):
>>
>> Order No. Site Height/Rms Grid Fractional coordinates
>> Orthogonal coordinates
>>
>> 1 1 1 128.24 0 0 0 0.0000 0.0000 0.0000
>> 0.00 0.00 0.00
>> 2 13 13 57.51 60 44 38 0.5000 0.2741 0.5000
>> 44.37 31.88 27.55
>> 3 2 2 33.75 0 7 0 0.0000 0.0414 0.0000
>> 0.00 4.82 0.00
>> 4 14 14 16.09 60 50 38 0.5000 0.3150 0.5000
>> 44.37 36.63 27.55
>> 5 12 12 15.75 60 37 38 0.5000 0.2324 0.5000
>> 44.37 27.03 27.55
>> 6 3 3 12.28 0 13 0 0.0000 0.0836 0.0000
>> 0.00 9.72 0.00
>> 7 15 0 7.06 60 57 38 0.5000 0.3574 0.5000
>> 44.37 41.56 27.55
>> 8 4 4 6.18 0 72 0 0.0000 0.4503 0.0000
>> 0.00 52.36 0.00
>> 9 9 9 5.68 5 0 5 0.0410 0.0000 0.0683
>> 3.64 0.00 3.76
>> 10 5 5 5.36 2 20 2 0.0142 0.1254 0.0206
>> 1.26 14.59 1.14
>> 11 11 11 5.33 58 31 38 0.4852 0.1909 0.5000
>> 43.06 22.20 27.55
>> 12 6 6 3.98 5 0 2 0.0435 0.0000 0.0286
>> 3.86 0.00 1.58
>> 13 7 7 3.82 2 27 3 0.0168 0.1659 0.0334
>> 1.49 19.30 1.84
>> 14 8 8 3.68 0 0 5 0.0000 0.0000 0.0722
>> 0.00 0.00 3.98
>> 15 10 10 3.41 60 64 37 0.5000 0.4007 0.4872
>> 44.37 46.59 26.84
>>
>> Phaser was used to test all possible alternative space groups to find
>> MR solution using the structure from P21 data:
>>
>> # Phaser_P222_MosFLM_all_spacegroup
>> SPACegroup HALL P 2bc 2 #P 2 21 21
>> SOLU SET RFZ=9.1 TFZ=24.3 PAK=0 LLG=2545 LLG=3718
>> SOLU 6DIM ENSE ensemble1 EULER 273.097 1.162 88.144 FRAC
>> -0.03394 0.50659 -0.22125
>> SOLU SET RFZ=9.1 TFZ=25.0 PAK=0 LLG=2496 LLG=3622
>> SOLU 6DIM ENSE ensemble1 EULER 91.491 0.850 89.812 FRAC
>> 0.03435 -0.00618 0.00352
>>
>> and it found 2 solutions with very similar Z-scores and LLG gains, If
>> I am right they are not crystallographic equivalent, and Phaser checks
>> that as well.
>>
>> I reindexed the data to P21212 and Phaser found the same solutions:
>>
>> # Phaser_Reindexed_P21212_2_solutions
>> SPACegroup HALL P 2 2ab #P 21 21 2
>> SOLU SET RFZ=10.0 TFZ=23.0 PAK=0 LLG=3266 LLG=3718
>> SOLU 6DIM ENSE ensemble1 EULER 88.843 90.063 1.249 FRAC
>> -0.00661 -0.22126 -0.46598
>> SOLU SET RFZ=9.9 TFZ=23.2 PAK=0 LLG=3178 LLG=3624
>> SOLU 6DIM ENSE ensemble1 EULER 270.841 89.977 181.339 FRAC
>> -0.50634 -0.00350 0.46533
>>
>> The difference between the two solutions seems to be that the second
>> solution translated along the longer 21 axis by about ~32Å, I chose
>> the first solution to re-build and refine, and final R/Rfree I got was
>> 21.6%/26.5%. After that, I hope to solve the ambiguity of which MR
>> solution is right by running Phaser again with the complete model
>> (including H2O):
>>
>> # Phaser_Reindexed_P21212_2_solutions
>> SPACegroup HALL P 2 2ab #P 21 21 2
>> SOLU SET RFZ=12.8 TFZ=28.4 PAK=0 LLG=6542 LLG=7649
>> SOLU 6DIM ENSE ensemble1 EULER 180.156 0.000 0.000 FRAC
>> -0.50060 -0.00065 0.49998
>> SOLU SET RFZ=12.8 TFZ=32.3 PAK=0 LLG=6036 LLG=7059
>> SOLU 6DIM ENSE ensemble1 EULER 179.201 180.000 0.000 FRAC
>> 0.00227 0.22262 -0.50054
>>
>> It seems that the previous first solution has become the second
>> solution, while the previous second solution became the first. Refmac
>> refinement was performed on both solutions (H2O removed) came out from
>> Phaser,
>>
>> solution 1 R/Rfree = 24.1/28.9
>> solution 2 R/Rfree = 24.8/28.7
>>
>> the previous first solution got slightly worse scores, however, the
>> R-factors for both solutions are so similar and both of them gave very
>> similar electron density that I can not figure out which one is the
>> right solution.
>>
>> I would very grateful for any advices.
>>
>> Thanks in advance,
>
>
>
>----------------------
>Xiaoli Xiong
>PhD Candidate
>Department of Cellular and Molecular Medicine
>School of Medical Sciences
>University of Bristol
>University Walk
>Bristol BS8 1TD, UK
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>
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