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Hi Rajesh, It might be water molecules present at the symmetry axis, one more water molecule at the centre (exactly at the axis, with occupancy of 0.5). If you put three water molecule you probably may find the other three symmetry-mates water molecules in opposite sides. OR One water molecule at the symmetry axis.surrounded by 5 different water molecules. Or You can try As Garib mentioned it may be a six anions (or water) coordinated with some metals possibly in crystallization or protein buffer. Please try refining both cases parallely. I once encountered such case in my structure. Probably it may help. Good luck Prem On Wed, Mar 7, 2018 at 4:37 AM, Abhik Mukhopadhyay <[log in to unmask]> wrote: > Hi Rajesh, > > You may find this database is also useful while refining your model > > http://mespeus.bch.ed.ac.uk/MESPEUS_10/ > > and for calcium > > http://mespeus.bch.ed.ac.uk/MESPEUS_10/_5.jsp > > Abhik > > On Tue, Mar 6, 2018 at 10:59 PM, Patrick Loll <[log in to unmask]> wrote: > >> Calcium likes to form octahedral complexes with water (or other >> oxygen-containing) ligands. This looks like a classic example. >> >> After you model and refine this, you’ll want to check water-metal >> distances, to make sure they are appropriate for calcium. There is a nice >> literature on such things, which I of course don’t have at my fingertips; >> but I think Wladek Minor has done some data-mining in metal-containing >> protein structures, and Amy Katz and Jenny Glusker have a number of papers >> that are relevant. There are more, of course—a little time in the “library” >> is warranted. >> >> Cheers, >> >> Pat Loll >> >> > On 6 Mar 2018, at 5:19 PM, Rajesh Kumar <[log in to unmask]> 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> >> > >> >> ------------------------------------------------------------ >> --------------------------- >> Patrick J. Loll, Ph. D. >> Professor of Biochemistry & Molecular Biology >> Drexel University College of Medicine >> Room 10-102 New College Building >> 245 N. 15th St >> <https://maps.google.com/?q=245+N.+15th+St&entry=gmail&source=g>., >> Mailstop 497 >> Philadelphia, PA 19102-1192 USA >> >> (215) 762-7706 >> [log in to unmask] >> [log in to unmask] >> > > -- With kind regards, Prem Prakash PhD Research Scholar Protein Crystallography Lab Biosciences and Bioengineering IIT Bombay