Dear CCP4 users,

I am working on a protein from a hyperthermophilic archaeon.

I have collected mutliple X-Ray datasets, both from home source and synchrotron and always found a clear density for tetrahedral geometry, co-ordinated by two histidines and one lysine. 

I tried fitting phosphate there, but its geometry always gets distorted after each refinement cycle (Refmac 5.8.0073). Also I found some short contacts between the coordinated residues and phosphate which were very difficult to remove.

I am attaching a figure with the density and phosphate. 

Kindly suggest -

1. if this may be a possible modification of any of the associated residues, and the code of the modified residue to be used.

2. If the ligand requires separate restraints during refinement, I am using the "restrained refinement" option available at the top of the GUI for refmac.

Thanking you,

yours sincerely,

Ansuman Biswas,

PhD student,

Dept. of Physics,

IISc