Re: [ccp4bb]: non-flat tyrosine

[Lisa Edberg <ledberg@uab.edu>]

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Out of plane tyrosines:

Such is fodder for the discussion section. Thank heavens for procheck
warnings!

I agree- look at the omit map, and use a minimization target that isn't so
sensitive to model bias, such as ML. A tyrosine can be slightly out of
plane, but look for a good reason- look at the packing and the steric
effects. The ring doesn't have to be completely flat for "resonance
stabilization", and far more important are deviations in bond lengths.  We
are looking at a time-averaged model. Look at the atomic displacement
parameters to see if they make sense. If the B's are small, and there's
something pushing on the one side, it could be real. Remember that the
macromolecule adopts a conformation that is a compromise of all the various
forces- everything can't be at ideal values simultaneously, and the whole
thing is in constant vibrational motion, anyway.

Lisa

--
Lisa Edberg (205)934-1611 FAX:(205)934-0480
UAB Center for Biophysical Sciences/Engineering
http://www.cmc.uab.edu/misc/edberg/index.html
"It's not always that Nature is being nasty to us.
Sometimes also we are stupid." -Thomas Schneider