Dear Dolphin,
That N- or C-terminal residues are not as well ordered as the rest of
the protein happens very often and is nothing to be concerned about,
especially if there is clear density at the 1 sigma level.
Prolines are rigid, but can exist in cis- and trans-conformation. I have
seen many cases where I strongly suspected that I was seeing a mixture
of cis- and trans-proline. Since these cases occurred in poorly ordered,
uninteresting parts of the protein, I did not go through the trouble of
trying to model them. In your case, I would try to model cis- and
trans-proline as alternative conformations as well as the flanking amino
acids. The electron density will tell if this is correct.
Best regards,
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Dolphin Huang
Sent: Tuesday, July 19, 2011 5:30 PM
To: [log in to unmask]
Subject: [ccp4bb] Poor proline electron density
Dear all,
Recently I crystallized and solved the structure of a protein using
molecular replacement. The crystal diffracts to 1.8A and has the R
free of 0.21. During refmac and phenix refinement, I found that the
N-terminal (~25 amino acids) electron density wasn't quite good,
especially a proline residue. It not only has little side chain
electron density, but also doesn't have continuous electron density
between backbone C-N until the sigma level going down until 1.2. A
normal backbone sigma contour level is above 2.5 in this structure. I
calculated composite omit map as well as the difference map. In
addition, NCS maps of those were calculated. But its density is still
unclear. As proline normally has rigid structure and good electron
density, will this mean some potential mistake in the structure?
There seems no other way to trace the backbone. And the upstream and
downstream residues are not that bad. If no way to find the solution,
could there be an explanation about the poor electron density of
protein. By the way, this proline is connecting a beta-sheet and an
alpha-helix, which is on the surface of the protein. Also, the protein
is soluble and has about 300 amino acids.
You kind suggestions will be greatly appreciated!
Dolphin
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