On Wed, 2021-03-31 at 19:48 -0400, Jessica Besaw wrote: > > I once again am asking for your advice. ☺ I am trying to solve the > structure of an RBD:Fab complex. > > After molecular replacement, the density fits the model very well. > Looking at the overall crystal structure (by applying symmetry mates > in pymol), I see large pores in the crystal with only little bits of > density as shown in the figure below. > > After doing refinement in phenix.refine, I now get these HUGE blobs > of density. But, they don't really interact with any part of the > structure, mostly just "floating" in the center, as shown in the > figure below. I have attached my current refinement strategy in case > I am choosing a poor strategy. > > Question: > (1) Are these blobs likely to be a protein? > (2) If it is not a protein, is there an honest / scientifically- > approved way to deal with these density blobs. I think they are > keeping my R values very high. > > Potentially useful information: > Rwork/Rfree = 27.1 / 30.1 > Spacegroup: P 32 2 1 > Highest Resolution: 3.35 Angstrom > Completeness: 99% (99%) > CC1/2: 0.99 (0.35) >
I imagine that the bulk solvent model/structure factor calculation/scaling is different between the first image and the second. Try blurring the first set of SFs by 90 A^2 or so and see if the blobs turn up to some extent. It does *seem* as if there is some connection to your model at about the 5 o'clock position of the left circle. This being CCP4BB, it is not inappropriate to suggest that you try another refinement program, one which has a different bulk solvent model (or a number of them from which to choose, even) to see if your blobs are recapitulated. So my answers to your questions are currently (1) I don't know, it's a close call (2) put atoms in them Paul. I always like "what's my blob?" questions. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
