Dear Cryosparc forum,
I have recently managed to push the resolution of a map i’ve been working on for a while to ~1.9 Å and I am now interested in assessing the nature of one of the ligands, that is luckily in an area of high local resolution of the map.
In particular, I can’t figure out whether one of it’s substituents is a methyl or a formyl group, since it could potentially be both, and atoms with a partial negative charge are in my experience less intense in signal.
In slightly lower resolution maps (~2 Å and ~2.1 Å), a density to fit the “extra” oxygen atom is present, but in the new high resolution structure said density seems to be less pronouced.
does anybody have any experience with a similar problem? are there any parameters that can be tweaked in the final non uniform refinement that might be helpful in clarifying this?
thanks for all the suggestions you might have and excuse me for the really niche question.
Gio