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Mischa Machius wrote:
If this approach was pushed to the extreme, it would imply that bulk
solvent atoms should also be explicitly included in the PDB file,
because, clearly "the atoms are in the crystal", e.g. refine hundreds
of bulk solvent atoms with occupancy = 1.0 and let the B factor
reflect the disorder....
The difference between the disordered water molecules you mentioned
and disordered lysine side chain atoms is that the lysine side chain
atoms are covalently connected to the rest of the protein. If C-beta
is well defined, we have a pretty good idea about where C-gamma is and
so on. Contour the 2Fo-Fc map at 0.3 sigma and you will likely see
some density. Whether this is noise or signal is a matter of
discussion (ask people in Tom Alber's lab), but at least refinement
programs have something to base their B values on.
So the criterion of atoms that should be modelled because they "are in
the crystal" has now been narrowed down to atoms that should be modelled
because they are "covalently connected to the rest of the protein".
If this concept is taken further, one could ask why we are not
explicitly refining hydrogen atoms ? Clearly, they are quite often
important for the biological function of a macromolecule. Clearly, they
are in the crystal, covalently connected to the rest of the protein and
we also have a pretty good idea about where they are.
But we are not refining hydrogen atoms because the experimental data
does not warrant this ! (unless we got very high-resolution data).
Shouldn't the same criterion apply for the refinement of disordered
non-hydrogen atoms ?
If we always had ultra-high resolution data, we could model and refine
many of the hydrogen atoms. But if the resolution of the data is
limited, we don't do that, event though we know that these atoms are
there. Similarly, if we had ultra-high resolution data, we could
possibly model and refine many of the disordered side-chains because the
low-occupancy alternate positions would probably show up in the maps.
But not so if the resolution of the data is limited.
--
Marc SCHILTZ http://lcr.epfl.ch
