[phenixbb] Gold atoms in cryo-EM

[a.malay at riken.jp]

Dear all,

I hope that this question is neither too off-topic or naive.

I am trying to refine a large protein structure against a cryo-EM map using Phenix real-space refinement. The protein complex is unusual in that the oligomeric state is held together via coordinated gold atoms. However, there seems to be a problem with refinement, in that the the gold atoms show extremely high B-factors (>200) after refinement, whereas the B-factors of the protein residues, including those surrounding the gold atoms, adopt more reasonable values.

My question is: could the unusually high B-factors of the gold atoms be somehow due to differences in the relative scattering of Au atoms when obtained from X-ray vs. electron beam irradiation? And if so, is there any way to correct for this? 

Thank you in advance for your kind help.

Best,
Ali