Re: [ccp4bb] positive density near asparagine

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 sidechi

Re: [ccp4bb] positive density near asparagine

Hello again, and thank you for your quick replies! For your consideration, I have added a representative .mtz and .pdb to my shared dropbox folder (https://www.dropbox.com/sh/2wdax5uqlb1f4m3/AABQlGK2_mgibtqnm61E-7o0a?dl=0).

Re: [ccp4bb] positive density near asparagine

If I've got the site right (the equivalent to Asn833 in your image would be Asn858 in 3rjo?) then the first thing I'd be checking is if you have an unmodelled tail or loop that could be interacting here across a symmetry interface. The dramatic kink in the helix there looks like an asparagine,

Re: [ccp4bb] positive density near asparagine

Hi, What is the highest resolution for your data? Depending on the resolution, do you see positive Fo-Fc peak which resembles the indole ring of Trp even if you have to lower the contour level of your Fo-Fc map a bit? What are the B-factors of the atoms of Trp for which there is a possibility of d

Re: [ccp4bb] positive density near asparagine

Hi Zach, It is hard to judge from one screen shot, maybe a double conformation of the Asn and the Trp immediately before it? Regards, Napo Em 2017-08-18 18:17, Maben, Zachary escreveu: > Hello, > > I am refining a few datasets of my protein of interest (ERAP1) bound to > various inhi

[ccp4bb] positive density near asparagine

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 sequ