Hello,
I suggest modelling the ligand as multiple conformations and also check
if some of the conformations are coupled with the surrounding
environment (side chains, waters, metals, etc.). Then, once you defined
constrained groups, refine occupancies and B-factors. In my experience
this works most of the time without too much effort.
Also, are you sure that the ligand you are fitting into that density is
actually the "right thing"? I mean, could it be a partial molecule - the
result of some reaction, or just a different ligand, or both, or both
plus some ions?
I can help you doing all this in phenix.refine
(http://www.phenix-online.org/). For this I will need more information,
such as data, model and ligand details. Please let me know.
Finally, at 2.6A resolution I'm not sure I understand what you mean by
"measuring the B factor".
Pavel.
On 5/11/10 8:07 PM, intekhab alam wrote:
Hi All
I solved one structure of a viral RNA polymerase in complex with some
ligands at 2.6 A resolution. The ploymerase structure has 3 monomers
in the asymmetric unit and in all the 3 monomers i found |Fo|-|Fc| as
well as 2Fo|-|Fc| map for the ligand. I tried to model my ligand there
and after putting that some naegative density propped up outside the
2Fo|-|Fc| map and also the postive density inside the 2Fo|-|Fc| map
didnt disappeared completely at 3 sigma (although it is reduced
significantly). I tried putting metals and other things there but most
of the positive density is gone only when i put my ligand there.
Besides these the ligand fits well only in one of the three chains at
1 sigma while in rest two it is around 0.8 sigma of |Fo|-|Fc| map. I
measured the B factor and findout that the B and C has higher B facors
(33) as compared to A (29). can anyone suggest me about how to improve
or fine tune my map around the ligand so that i can get rid of this
positive and negative density (i already have tried different binding
modes.
Thanks
--
INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL
