Dear all, thank you for the valuable inputs. I realize that one important piece of information that must be added concerns the relative orientation of the domain for which the electron density becomes poor upon merging data towards higher symmetry, with respect to the rest of the protein.
We have found that, at the monoclinic symmetry, this domain can be safely located for 6 of the 20 monomers in the asymmetric unit. By safely located, I mean that these 6 copies were automatically positioned by Phaser and refined well throughout. On the other hand, for the remaining 14 copies, not even manual positioning worked. At the tetragonal space group, neither of the 5 copies for this domain refine well, after borderline MR solutions for 2 copies. Therefore, based on your responses I understand that, while the indication of twinning in P21 may be misleading, P42212 can be a case is a pseudo symmetry. The intrinsic flexibility of this domain, as a rigid body, is however most properly resolved in the P21 symmetry. I will soon try refining again in P21 without imposing twinning. If the quality of the electron density map for the domains is reproduced, with and Rfree in the range of 30-ish%, this would be a more correct approach, right? I will make sure I incorporate all you suggestions in this subsequent analysis. As a matter of fact, xtriage concludes that twinning is not indicated or not possible for the P42212 sg. Thank you again and kind regards, Andre. -----Mensagem original----- De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Em nome de Kay Diederichs Enviada em: terça-feira, 6 de dezembro de 2016 14:06 Para: CCP4BB@JISCMAIL.AC.UK Assunto: Re: [ccp4bb] Choosing test set for twin refinement, with multiple operators Hi Andre, you should first optimize your data processing as much as possible ... try different programs, and do test refinements against the data they give you. Unfortunately Rwork/Rfree is a poor indicator unless the Wilson B is the same; what is much more robust is the correlation coefficient CCwork/CCfree as a function of resolution. If you get 25% Rfree in twin refinement in a low-symmetry spacegroup with equal twin fractions, and 33% in the high-symmetry spacegroup without twin refinement, then the high-symmetry spacegroup may be the correct one. As Phil says, the intensity stats may be skewed due to close spots. To answer your question: for an unbiased free set, assign the free reflections in the high-symmetry space group and expand them (using sftools or similar) to the low symmetry space group. best, Kay
