On Apr 15, 2010, at 10:08, Thomas Lütteke wrote:
Dear Katherine,
I would like to add a futher point to this discussion: If you do
model residues with poor or no electron density, then you should be
sure of what you are doing and not just make more or less unguided
guesses. This seems obvious but unfortunately it isn't, at least not
to everybody. For example, I recently found a PDB entry of a
glycoprotein that had an a-L-IdopNAc residue attached to an Asn side
chain. Usually the first monosaccharide linked to an Asn is b-D-
GlcpNAc -- there are only very few exceptions to that. Therefore, I
had a look at the electron density and I saw that only part of the
ring was resolved there; around the C5 atom of the sugar there was
no electron density. b-D-GlcpNAc and a-L-IdopNAc only differ in the
stereochemistry of the C5 atom, so it seems to me that the
crystallographers arbitrarily placed the C6 and O6 somewhere and
picked a wrong position, which led to wrong stereochemistry of the
C5 atom. (This is in principle the same as adding an Ala CB atom
somewhere near the CA atom and picking a position resulting in D-Ala
instead of L-Ala.) In the example above it would have been better to
leave out the unresolved atoms rather than creating an obviously
wrong model, I think.
Wouldn't it be even better to use to correct the restraints to keep
the stereochemistry? If we relax the Cbeta stereochemistry, I bet we
can end up with a few L- residues as well ...
A.
The problem of non-crystallographers non knowing about occupancy or
B-factors might be solved (in part) by better pointing out
"problematic" parts of the structures, e.g. by highlighting them in
visualization tools by default and not only when the user sets color
mode to "temperature" or something like that.
Cheers,
Thomas
P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
