I am trying to build a model of a 60000 Da protein from the
diffraction data collected at 2.0 A resolution. There is a 10-residue
stretch that has such bad electron density that even at 0.4 sigma level
one can hardly see any well defined density for residues with long side
chains.
My question is: are such poorly defined regions left unmodeled in
protein structures? Or is it conventional to model the whole chain no
matter how poor the density? The region in question is in the middle of
the chain and has several long side chain residues - both charged and
uncharged.
AM
