Dear all,
I am at the late stage of refining a 1.97 A structure. There is something
in the ligand binding pocket, and I am not sure what it is exactly. Since
this protein can potentially generate pyrophosphate from ATP, and I have
ATP in the protein solution, so I tried to fit in a pyrophosphate. The
Rwork/Rfree after refinement are 0.198/0.243. Below is the refined map. The
2fofc map looks ok (contoured at 1 sigma), however, there is always some
red density around the pyrophosphate in the fofc map (contoured at 3
sigma). I have also tried to fit in the density as two free phosphates, and
the results are worse. Can I get some advices on this? Any suggestion will
be greatly appreciated.
Best regards,
Junyu
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