The twinning factors all about 0.25 do point to a higher symmetry than P21. As others say - I would be very surprised (and would question result as a referee) if your FreeR was not >> 30% for such low resolution data
Is the data anisotropic - often is with such a long cell edge.. If so do process to the highest possible resolution in the a b orientation - the quality indicators will be much higher with aniso data and you may be throwing away good measurements . Eleanor On 6 December 2016 at 14:37, Andreas Forster <[email protected]> wrote: > Dear Andre, > > I agree with Jacob that P 42 21 2 might be the right space group, and that > and R free of 33% isn't so bad. If your electron density is poor, that > might just reflect the low resolution. Have you tried refinement with > Buster? It has a way with low-resolution data. > > All best. > > > Andreas > > > > On Tue, Dec 6, 2016 at 3:25 PM, Keller, Jacob <[email protected]> > wrote: > >> What were the twinning tests like in p42212? I suspect that it is really >> that spacegroup, the low Rfree is artificial (33% is not too bad at 3.9 >> Ang) and the electron density is bias. >> >> >> >> JPK >> >> >> >> *From:* CCP4 bulletin board [mailto:[email protected]] *On Behalf Of >> *Andre Luis Berteli Ambrosio >> *Sent:* Tuesday, December 06, 2016 9:17 AM >> *To:* [email protected] >> *Subject:* [ccp4bb] Choosing test set for twin refinement, with multiple >> operators >> >> >> >> Dear all, >> >> We are currently refining a low resolution model (3.9 A max), obtained by >> MR. Dataset was collected from a single crystal with one long cell axis >> (~620 A) and high solvent content (74%). >> >> Best refinement results (by far!) are obtained in Refmac, by imposing P21 >> sg (20 multidomain monomers/AU) and allowing for amplitude-based twin >> refinement. >> >> Accordingly, Refmac identifies four twin operators, which I understand >> have considerable fractions, as follows: >> >> >> >> **** Twin operators with estimated twin fractions **** >> >> >> >> Twin operator: H, K, L: Fraction = 0.249; Equivalent operators: -H, >> K, -L >> >> Twin operator: -H, -K, L: Fraction = 0.260; Equivalent operators: H, >> -K, -L >> >> Twin operator: -K, -H, -L: Fraction = 0.235; Equivalent operators: K, >> -H, L >> >> Twin operator: K, H, -L: Fraction = 0.257; Equivalent operators: -K, >> H, L >> >> >> >> I suspect that the low Rfree (~25%) may be artificial and results from an >> inappropriate selection of the test due to the multiple operators. >> >> However, I cannot figure out how to properly select the test set when >> such a high number of operators must be considered. >> >> FYI, space group P42212 resulted in the best processing statistics (5 >> monomers/AU); however, model never improved from an Rfree of 33%, with the >> quality of the electron density distribution for some of the domains being >> heavily compromised. >> >> I honestly apologize if I am missing some obvious points here and will be >> happy to provide more info, including statistics on data processing. >> >> Since is a multidomain protein, is it also appropriate to include TLS >> refinement at this low resolution? >> >> I thank you all in advance. >> >> Best, >> >> Andre. >> >> >> >> >> >> >> >> >> > >
