Thank you Kendall and Pavel for your responces.
I really want to determine the occupancy of my ligand. I saw one suggestion to
try different refinements with different occupancies and compare the
B-factors.
The occupancy with a B-factor that is at the
level with the average protein B-factors, is a "true"
occupancy.
I also noticed the dependence of
the ligand occupancy on the initial occupancy. I saw the difference of 10 to
15%, that is why I am wondering if the second digit after the decimal
point makes any sence.
Maia
----- Original Message -----
Sent: Tuesday, November 24, 2009 8:22
PM
Subject: Re: [phenixbb] occupancy
refinement
Hi Maia,
I think the criteria for occupancy
refinement of ligands is similar to a decision to add an alt conformation for
an amino acid. I don’t refine occupancy of a ligand unless the
difference map indicates that we have to. Sometimes part of the igand may be
conformationally mobile and show poor density, but I personally don’t think
this justifies occupancy refinement without evidence from the difference map.
I agree with Pavel that you shouldn’t expect much change in overall
statistics, unless the ligand has very low occupancy., or you have a very
small protein. We typically see 0.5-1% difference in R factors from
refining with ligand versus without for nuclear receptor igand binding domains
of about 250 amino acids, and we see very small differences from occupancy
refinement of the ligands.
Regarding the error, I have noticed
differences of 10% percent occupancy depending on what you set the starting
occupancy before refinement. That is, if the starting occupancy starts at 1,
you might end up with 50%, but if you start it at 0.01, you might get 40%. I
don’t have the expertise to explain why this is, but I also don’t think it is
necessarily important. I think it is more important to convince yourself that
the ligand binds how you think it does. With steroid receptors, the ligand is
usually planer, and tethered by hydrogen bonds on two ends. That leaves us
with with four possible poses, so if in doubt, we will dock in the ligand in
all of the four orientations and refine. So far, we have had only one of
several dozen structures where the ligand orientation was not obvious after
this procedure. I worry about a letter to the editor suggesting that the
electron density for the ligand doesn’t support the conclusions of the
paper, not whether the occupancy is 40% versus 50%.
You might also
want to consider looking at several maps, such as the simple or simulated
annealing composite omit maps. These can be noisy, so also try the kicked maps
( http://www.phenix-online.org/pipermail/phenixbb/2009-September/002573.html),
which I have become a big fan of.
Regards,
Kendall
Nettles
On 11/24/09 3:07 PM, "chern@ualberta.ca"
<chern@ualberta.ca> wrote:
Hi,
I am wondering what is the criteria for
occupancy refinement of
ligands. I noticed that R factors change very
little, but the ligand
B-factors change significantly . On the other
hand, the occupancy is
refined to the second digit after the decimal
point. How can I find
out the error for the refined occupancy of
ligands?
Maia
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