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Dear all,
I was wondering what the most acceptable way to
deal with (disordered) sidechains/residues (e.g. sidechains
of Arginines and Lysines) with very low or no electron density
is? Especially with respect to submission of coordinates to the pdb-data
bank.
My initial approach was to set the
occupancies of the atoms to 0 and then refine in Refmac. However I
encountered that the geometry (bond lenghts and angles) gets distorted between
the atoms with normal occupancy and the ones with zero occupancy. The other
option to refine the residues as alanines does not seem a very good
idea to me, since it does not account for something which is
there, but strongly disordered. For me the most ideal way to deal with
them is to fix the B-factor to a very high value and then refine with
Refmac.
What is the general opinion about this
matter?
I would be grateful for any
comments.
Thank you,
Florian
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Florian Schmitzberger University of Cambridge Department of Biochemistry 80 Tennis Court Road CB2 1GA Cambridge Tel: 0044-1223-766029 |