Re: Residual density around iron

[Bart Hazes <bart@sherlock.mmid.ualberta.ca>]

*** unsubscribe by sending the message "unsubscribe ccp4bb" to   ***
***       ccp4bb-requests@dl.ac.uk  or  Majordomo@dl.ac.uk       ***

Dear Alexander,

I can think of two causes for the effect you see.

1) The refined B-value is too low. This could give a negative peak at the
iron position and a positive density sphere around it. I don't think this
is very likely, but I mention it because I have had problems refining
B-values of "heavy" atoms (copper) with XPLOR in the past. I found that
XPLOR gave a "convergence reached" message too soon. The protein B-values
had maybe converged, but the coppers were still way off (160 instead of
the correct 12). The solution was to set the tolerance to 10E-7 or some
other very small number to force XPLOR to keep on refining.

2) Fourier ripples. For my copper protein, hemocyanin, we had a data set
to 2.18 Angstrom resolution. This was the resolution limit of the
detector, not the crystal. That means that we still had relatively strong
data all the way up to the resolution limit. The sudden truncation at 2.18
Angstrom gave Fourier ripples in the map which were very noticable around
the coppers. In a difference map there were alternating spheres of
positive and negative density around the coppers. This may be what you see
too.

Bart Hazes