CCP4 bulletin board <[log in to unmask]> wrote on 03/07/2009 07:11:20
PM:
> Hi All,
>
> Sorry if this is a trivial question. I'm refining my first structure
> at 2.1 A resolution. There is no density for the main chain carboxyl
> oxygen of a residue even at 0.5 sigma level in 2FoFc map. The FoFc
> map shows a negative density when I place the oxygen, satisfying the
> standard geometry condition. Could someone tell me what to do in this
> situation. Should I make the occupancy of the oxygen zero. Any
> comments would be gratefully appreciated.
>
> Thanks very much.
>
> John Peter
Hi John Peter -
Is there a positive density peak on the other side of the peptide group?
It's quite common to have the peptide bond flipped 180 degrees from the way
it should be. The nitrogen atom doesn't move much, so you usually don't
see difference density for it, but the oxygen atom moves a good deal and
gives difference density peaks. (As others have noted, I'm assuming you
meant carbonyl oxygen - the one in a peptide bond - not carboxylate oxygen
- the one at the C terminus.)
I don't really know about other refinement programs except O, but there
should be some sort of "flip peptide" command - if not, you'll need to move
things manually. Just so we're clear, I'm talking about turning this:
H
Ca-N-C-Ca
O
into:
O
Ca-N-C-Ca
H
Check hydrogen bonding patterns to see if the flipped peptide group makes
sense chemically, of course.
- Matt
--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems,
a wholly owned subsidiary of Eli Lilly & Company
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116 fax:(212)645-2054
Confidentiality Note: This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail. If the reader of this e-mail
is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited. If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system. Thank you.
|