Quoting Dale from an older post "It's also true that the Wilson B calculation assumes that all the B factors in the crystal are the same - which is also far from the true in most macromolecular crystals. A person who holds to the practice of aggressively building water molecules and loops will create a model with a higher average B than one who uses the same data but is more restrained. The Wilson B will, of course, be unchanged. If you have a protein that is equally ordered throughout and you do not build in weak water molecules and the crystal diffracts high enough to allow a reasonably accurate calculation of the Wilson B, your average B and and the Wilson B should be close to each other. If your protein has mobile loops, which most lower resolution crystals do (and most higher resolution crystals for that matter) then your average B will be larger than your Wilson B."
This kinda agrees with my scenario I think... Wilson B is 83 A*2 and Av B 98 A*2, the discrepancy contributed by mobile loops? (3.0 A resolution). Refinement with group B factors (two per residue) brought the av B down to 80 A*2. TLS, PDB_REDO etc did not help much. I got the model by Mol Rep, have not tried PROSMART... And I agree with Phoebe...The aa's are fully there! Lowering the occupancy may work with Hetatms, but doesn't make sense to do it with residues! On Fri, Oct 14, 2016 at 9:08 PM, Phoebe A. Rice <[email protected]> wrote: > Interesting way to look at it. But those loop residues are really in the > crystal with an occupancy of 1, so wouldn't letting the B factor fly give a > clearer description of what's in the crystal? Especially as many people > know to color the structure by B factors to get a feel for which bits are > wiggly, but they'll never think to color it by occupancy. > > ------------------------------ > *From:* CCP4 bulletin board [[email protected]] on behalf of Matthias > Barone [[email protected]] > *Sent:* Friday, October 14, 2016 8:00 AM > *To:* [email protected] > *Subject:* [ccp4bb] Antw: Re: [ccp4bb] High B factor > > Picking up the mail of Pavel, Phenix refines occupancies.. > If you expect the loops to be disordered, did you try to lower the > occupancy of these residues, following Ethan Merritt statement that > "general uncertainty [...] is represented better by occupancy <1 rather > than an arbitrary large B factor" (To B or not to B, > doi:10.1107/S0907444911028320). > If this attempt does not bring the B-factors down, it will surely make the > model more accurate, as the atom coordinates of the loops may not be > correct at all, no? > > matthias > > > >>> Pavel Afonine <[email protected]> 14.10.16 9.36 Uhr >>> > > If you are still worry about your Bfactor, you could try TLS, >> > > Or NCS, but SA with MLHL might be better. > > (A joke). > >
