Hi Dilip,
There are a few things you might try. You have to make sure that all coordinating atoms (including waters) are in your model. If you refined with TLS for the protein, try resetting the B-factors for all atoms and refine without TLS. If this reduces the difference density, you could also try including your metal atoms in the TLS group of the protein. In some cases the metal ions have anisotropic density. You could try refining anisotropic B-factor for just the metal ions. Cheers, Robbie From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Dilip Kumar Sent: Thursday, July 9, 2015 11:35 To: [email protected] Subject: [ccp4bb] Ambiguous metal ion at active site. Dear All I have solved a structure of a metal-ion dependent exonuclease enzyme. In homologous structures, two or three Manganese ions are present at catalytic center. However, I have used 2 mM MgCl2 in protein purification buffer. I tried to fit both of these metal ions at catalytic center but in both cases it still shows green density (Sigma level ~ 7) in difference map and low b-factor (<10) for these metal ions. For better understanding I have attached the screenshot of metal ions with difference map on. Please suggest me the possible reasons or methods to validate the presence of any other metal ions at catalytic center. Thanks in advance. Regards Dilip Kumar Research Associate Chemical and Systems Biology Unit CSIR-Institute of Genomics & Integrative Biology Delhi-110025
