What is the height of non-origin Patterson function peak for your data sets?
C-centered cells:
216.5 345.8 145.2 90.0 90.0 90.0
and
147.0 354.3 217.4 90.0 90.0 90.0
are very different; however, they have common subgroup F222 with similar
unit cell parameters. In F222 one can permute the unit cell axes while
preserving symmetry operators.
For these C centered cells to have approximate F222 subgroup they need to
have pseudotranslational symmetry that can be detected by calculating the
Patterson function. You should have strong reflections with all indexes
even or odd, and other reflections being weaker. What is the spot shape of
these weaker spots?
In case of pseudotranslational symmetry, MR can produce a pseudosolution
related to the correct one by pseudotranslational symmetry vector.
Translate your C2221 solution by {0, 0.5, 0.5} and try refining again.
Zbyszek Otwinowski
> Dear Veronica,
>
> with 1st, 2nd, 3rd map you mean the density for the same dataset after
> three consecutive cycles of building-refining or three different maps from
> three different crystals?
> If it's the first case, it could be fine, it may mean that at each cycle
> you improve the map so you see signal from the different ligand molecules.
> If it's the second case, well, it could be simply an artifact. Are the
> ligands proximal one to another or bind different sites on the protein?
>
> Best
> V.
>
> 2016-10-26 14:32 GMT+02:00 Veronica Fiorentino <
> [log in to unmask]>:
>
>> Hello all,
>> I just solved a NCS-tetrameric (biological assembly is just a dimer)
>> crystal structures with ligand soak (same plate - same conditions). No
>> density for ligand is observed in the first map. In the 2nd, I have 1
>> ligand bound. In the 3rd, I have 2 ligands bound. Is there any reason
>> for
>> this 'random' behaviour?
>>
>> In addition, I observed just one crystal out of 20 gave a different unit
>> cell. Pointless confirms to me
>> "Best Solution: space group C 2 2 2". REFMAC refinement shows R/Rfree
>> ~
>> 20/25 %
>> Cell from mtz : 216.5 345.8 145.2 90.0 90.0 90.0
>> Space group from mtz: number - 21; name - C 2 2 2
>>
>> All other datasets have:
>> Cell from mtz : 147.0 354.3 217.4 90.0 90.0 90.0
>> Space group from mtz: number - 20; name - C 2 2 21
>>
>> I tried re-processing/refining the C2221 dataset in C222 but R/Rfree
>> stays
>> ~45%. Can I also consider the C2221 dataset as a 'different crystal
>> form'?
>>
>> Am I safe?
>>
>> Thank you all,
>> Veronica
>>
>
>
>
> --
>
> *Valentina Speranzini, PhD*
> European Molecular Biology Laboratory
> Grenoble Outstation
> 71, avenue des Martyrs, CS 90181
> 38042 Grenoble Cedex 9, France
> Web: http://www.embl.fr
> E-mail: [log in to unmask]
> Tel: +33 (0)4 76 20 7630
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
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