Hi Lisa,
Why are you so sure there are 4 molecules in the ASU?
There may only be 3 and forcing a fourth molecule is causing lots of clashes. In
a similar case, I have seen phaser put two molecules right on top of each other
when I forced it to search for too many molecules.
In your case I would look at the solution (crystal
packing) in coot and see whether the clashes are due to some loops (or
domains) which may move upon ligand binding, or whether one of the
molecules is at a completely wrong position and if you get a good crystal
packing (crystal contacts in all directions) with fewer
molecules. You can also start refinement with fewer molecules and see if
additional density for missing molecule(s) appears.
Good luck!
Herman
Hi all,
I am trying to solve one structure by molecular
replacement with phaser in CCP4. This a complex of a multi-domain
domains with small ligand. I have structues of this protein in apo state and
with other similar ligand. The space group of this crystal is P21. This
crystal should have 4 molecules in ASU. I used the full protein as model
but did get any sol and LLG is below zero. Then each domain were used as the
search models in phaser with rotation and tranlsation. I can the get high z
score (>20), and LLG is raising. It looks like I get the right sol, but
it have more 50 clashes. Why phaser give wrong sol with so high z
socre? Can anyone give me some suggestion to solve my strucutes? Thank
you.
Best
Lisa