You could try to put CA (as you have CA in your crystallisation condition) and waters for coordinating atoms. If after refinement distances are around 2.3-2.4 (if I remember correctly) and B values of atoms (CA and waters) are consistent, i.e. similar to each other then CA is good interpretation. Similarly you could use MG (but since this atoms does not seem to be involved in structure or function it is unlikely to be part of your protein, it should come from crystallisation, purification etc, so MG is less likely than CA) and the distances are around 2-2.1A and (again) B values are consistent then MG is good.
Regards, Garib On 6 Mar 2018, at 22:37, Hussain Gps <hussain...@gmail.com> wrote: > Hi Rajesh, > > Can you please let everyone know the buffer/reagents involved throughout the > process. > > Also, how strong is the density? In other words, until what contour level you > see it in the Fo-Fc map? > > Anyways, looking at the shape, it looks well coordinated - could be > cacodylate? Or water, am not sure. > > Cheers, > Hussain > >> On 7 Mar 2018, at 9:19 am, Rajesh Kumar <rajesh.p...@gmail.com> wrote: >> >> Dear All, >> >> Have you had experience with this kind of density? I am wandering what this >> could be? >> >> Thank you very much for the help. >> >> -Rajesh >> >> >> <Screen Shot 2018-03-06 at 5.15.20 PM.png> >> Dr Garib N Murshudov MRC-LMB Francis Crick Avenue Cambridge CB2 0QH UK Web http://www.mrc-lmb.cam.ac.uk, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/