before modelling a long side-chain in non-existing or dubious density,
also make sure it is really there in the protein by sequencing your
expression plasmid. Your arginine (for example) may in fact be a
serine or glycine...databases are not 100% accurate and neither is PCR
if it was used
Dear all
i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22
and 25 respectively..the Ramachandran plot shows 90% of the residues in the
most favorable region and with 6 residues in generously allowed and no
residues in disallowed region. But in some areas i can see density
Hi,
There has been quite a lot of discussion about this and I think
different opinions exist. I would try to keep the side chains, if
there is some evidence where they are. Otherwise I would just delete
atoms and I would not mutate them to alanine.
On Friday, 09 November 2012, Faisal Tarique wrote:
Dear all
i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22
and 25 respectively..the Ramachandran plot shows 90% of the residues in the
most favorable region and with 6 residues in generously allowed and no
residues
Dear Faisal,
You definitely do not mutate to alanine as that would imply for the
future user of your pdb file that it is a mutant.
Some people feel they have to keep the side chain but put the
occupancies at zero. I think this is a bad practice and strongly oppose
to it as for the future
