Hi Wei,

I think it might be good (as you imply) to wait to place your ligands until you have the rest of the molecule almost as good as it can be.  That will help in the placement of the ligands and in avoiding putting them in noise peaks. It may also help in getting the rest of the molecule out of the way of the ligand (perhaps the ligand is moving out of density because it is too close to some atoms from the rest of the molecule).

All the best,
Tom T


From: [email protected] [[email protected]] on behalf of Wei Shi [[email protected]]
Sent: Thursday, October 24, 2013 8:19 PM
To: PHENIX user mailing list
Subject: [phenixbb] protein-ligand complex structure

Hi all,
I am working on a structure of protein-ligand complex. Four ligands are placed for the dimer protein and the density for the two ligands of the first monomer is better than the density for the other two ligands of the second monomer. Ligand is moved to fit density better in Coot (and for two ligands of the first monomer, they fits the density almost perfectly), but after a refinement in phenix (default settings + NCS restraints + Secondary structural restraints + Optimize X-ray/stereochemistry weight +Optimize X-ray/ADP weight), some part of the ligand which fits density good before moved out of the density again...Besides, it always shows green density in Coot for the ligand region even in places where the ligand is in density...
Any suggestions or ideas about how to fit the ligand better and why the density for ligands of the second monomer is worse than that for the first monomer and why the ligands would move out of density after refinement?
Is it because the protein model is not good enough to get the ligand density good? There is a conformational change upon ligand binding, and I rebuilt some part of the protein manually, and the density for a region of about 30 residues is not very good, and I tried to mutate those to alanies and refine, but it didn't help me see the density better...
Any suggestions or ideas on how to improve this protein-complex structural model?  Thank you so much!
The statistics for the current best model is as follows, and the resolution of the dataset is 2.8Å.

                           start         final
  ------------------------------
----------------
  R-work:           0.3359        0.2993
  R-free:             0.3619        0.3558
  RMS(angles):     1.03           1.55
  RMS(bonds):    0.006          0.007

MolProbity validation
Ramachandran outliers:   4.7% (Goal: < 0.2%)
Ramachandran favored:  85.3% (Goal: > 98%)
Rotamer outliers:   4.5% (Goal: 1%)
C-beta outliers:   0    (Goal: 0)
Clashscore:   7.43
Overall score:   2.56

Thank you so much!

Best,
Wei