Hi Zach, It seems the residues which you are discussing belong to an helix. It is not clear what is the present Rfree, however the residues side chains are not properly fitting. Did you use real space refinement in coot using helix secondary structure constraints? Hopefully it will push Asn sidechin in residual electron density and Trp will also get a proper fit in 2Fo-Fc. Thank you. Anurag
On Aug 18, 2017 16:28, "Maben, Zachary" <zachary.ma...@umassmed.edu> wrote: > Hello, > > > I am refining a few datasets of my protein of interest (ERAP1) bound to > various inhibitors, and I repeatedly observe a positive density peak near > an asparagine. I first thought this might be a glycan, but this site does > not fit the canonical N-linked glycosylation motif (this site sequence is > NKL). Previous crystal structures of this protein do not identify any > ligand at this position. > > > https://www.dropbox.com/sh/2wdax5uqlb1f4m3/AABQlGK2_mgibtqnm61E-7o0a?dl=0 > <https://www.dropbox.com/sh/2wdax5uqlb1f4m3/AABQlGK2_mgibtqnm61E-7o0a?dl=0> > Asn833 positive density > <https://www.dropbox.com/sh/2wdax5uqlb1f4m3/AABQlGK2_mgibtqnm61E-7o0a?dl=0> > www.dropbox.com > Shared with Dropbox > > I would appreciate any suggestions of what this density might be. Thank > you for your help. > > > Best, > > Zach Maben > > Stern Lab > > Pathology Department > > University of Massachusetts Medical School > > > <https://www.dropbox.com/sh/2wdax5uqlb1f4m3/AABQlGK2_mgibtqnm61E-7o0a?dl=0> >
