Hi Kavya,
If I understand you correctly (from title and text), you meant your negative
FoFc was around your ligand, is that right? I wonder if this is a case in
which the ligand has an occupancy below 1, but was modeled as 1, so the
refinement program had to give it a high B factor to compensate that, which
results in the electron density bleeding into nearby space where there
should not be so much of it.
If you want to test this hypothesis, one thing you can try is to set the
occupancy to 0.25, 0.5,0.75 and so on, and refine a few cycles to see what
happens to the maps. Also, what's the B factor of the ligand, and what's the
B of the nearby protein atoms? The difference between them can also give you
some hint for guessing the ligand's occupancy. Some refinement
programs(phenix.refine and shelx) can also let you refine the ligand's
occupancy.
As to the "missing" atoms, that could be caused by alternative conformations
of the ligand - assuming you have already done a thorough refinement.
Zhijie
--------------------------------------------------
From: "Kavyashree Manjunath" <ka...@ssl.serc.iisc.in>
Sent: Friday, May 24, 2013 12:50 PM
To: <CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] Negative FoFc around ligand
Dear users,
I am using refmac 5.7.0029 for refining a structure (resolution 2.2 Ang)
bound to 2 ligands. After MR There is a very clear density of ligands but
after refinement, I get negative fofc map near one of the ligand upto 5
sigma. However its 2fofc map covers the whole ligand. Also for the other
ligand, I do not see any 2fofc density (at 3 sigma) for 2 atoms, without
these atoms the ligand is unrealistic. But the density comes up around
these at around 0.7 sigma.
Overall completeness is 99.9%
Rmerge 7.5%
What else I need to check in the data. Kindly provide some suggestions.
Thanking you
Regards
Kavya
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