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
