Hi Ali,
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?
- have you tried re-setting B-factors of gold to small(er) values (say similar to surrounding atoms) and then re-running refinement? - did you make sure to use 'electron' scattering table (default is for X-rays)? Use scattering_table=electron for this. - have you tried to convert the map into structure factors (generally not recommended! but in this case worth trying as part of investigation) and then use B-factor refinement (only) (so it runs faster) in phenix.refine? If none of the above gives a clue then I may need to investigate deeper and that will likely require me having all relevant files (map, model etc). Pavel