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 <kell...@janelia.hhmi.org> 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:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Andre > Luis Berteli Ambrosio > *Sent:* Tuesday, December 06, 2016 9:17 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *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. > > > > > > > > >
