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 double conformation? Same for Asn. Even at 1 sig., the sidechain of Asn doesn't really seem to fit into the 2Fo-Fc map. Also, the positive peak near Asn seems to be very prominent and I am not sure if a misplaced sidechain can give to such a prominent positive peak. This is again subject to the resolution of your data and the degree of disorder for the Asn sidechain. Also, what are the components of your crystallization and cryoorotectant solutions? It might be possible to give more detailed comments if you can share your structure factor data and co ordinates.
Best, Tushar. On 19 August 2017 at 04:50, Napoleão <n...@unb.br> wrote: > 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 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 > > > > -- Tushar B. Raskar Graduate student, 49A/106, Pearson Lab, Centre for Free electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg.
