There is another possibility that your ligand is not fully occupied,
if the binding site of protein endures an apparent change when bound
by ligand. Lijun
On Dec 28, 2007, at 7:55 AM, Brenda Patterson wrote:
Hello,
I am fairly new to this lark so please forgive me if this question
is unclear,
but it is really puzzling me.
I have used phaser to generate a molecular replacement structure of
my target
(which has 100% identity to my template) and this particular
crystal I had
soaked with a ligand.
I have a density in my difference map which resembles my ligand.
The thing is,
it overlaps the density map of my structure and if I were to place
the ligand
in that map, then there would be a steric clash. Obviously I would
expect the
ligand to be near to the structure, but not overlapping it? I am
uncertain how
to proceed?
Any helpful suggestions please?
Thanks in advance
Brenda
Lijun Liu, PhD
Institute of Molecular Biology
HHMI & Department of Physics
University of Oregon
Eugene, OR 97403
541-346-4080
