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 2.8
Å. 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