I would use a very general definition for "solvent",
including disordered detergent and lipids.
As you know in many cases ordered detergents and lipids
have been modeled in the coordinates, so they are part of
the model not the solvent. In some cases I think waters
should be included in the model not solvent- say for
structural waters buried in the protein at least.
Ed
Savvas Savvides wrote:
Dear colleagues,
in estimating the solvent content of membrane protein crystals it would
only seem reasonable that micelle size should also be taken into
account. Depending on the aggregation number and MW of a given
detergent, the concentation of detergent used, and the buffer
conditions, one may have micelles on the order of 15-25 kDa or even
35-50 kDa for detergents with alkyl chains of more than 10 carbons.
However, when I took a look in a handful of papers reporting Matthews'
numbers for membrane protein crystals, it became apparent that only the
protein MW is used in such estimates. I am beginning to wonder if one
should even bother reporting a Matthews number for a membrane protein
crystal given the uncertainties surrounding size and role of micelles
in crystal packing.
Any thoughts on this?
best wishes
Savvas
