Recently, I collected a dataset of a protein-DNA complex and indexed in spacegroup P212121 to 3.4 Å. However, Phenix.Xtriage indicated the presence of a very high pseudotranslational symmetry peak. I scaled the data in spacegroup P222. When I used the protein heterotetramer as search model to do the MR, solutions are suggested in P22121, P212121, P2212, P21212 and all with a TFZ score higher than 15, LLG higher than 570. Then I used phenix.refine to refine those solutions; however the Rfree is as high as 0.54-0.56. The refinement strategy that I used for the refinement is rigid body, group B-factors and XYZ coordinates.
How to deal with this pseudotranslational symmetry problem? Does a solution with such high TFZ scores mean that the correct one has been found? How to solve the spacegroup problem in such situation?
Do you have any suggestions?