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.
On Wed, Mar 7, 2018 at 4:37 AM, Abhik Mukhopadhyay <abhik.jour...@gmail.com>
> Hi Rajesh,
> You may find this database is also useful while refining your model
> and for calcium
> On Tue, Mar 6, 2018 at 10:59 PM, Patrick Loll <pjl...@gmail.com> 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.
>> Pat Loll
>> > On 6 Mar 2018, at 5:19 PM, 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>
>> 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
>> Mailstop 497
>> Philadelphia, PA 19102-1192 USA
>> (215) 762-7706
With kind regards,
PhD Research Scholar
Protein Crystallography Lab
Biosciences and Bioengineering