[buster-discuss] Bulk solvent model

Kenneth Verstraete Kenneth.Verstraete at UGent.be
Wed Feb 16 16:38:39 CET 2011

Dear all,

I have been working on the low resolution refinement (4.3 Angstrom) of
a complex with autoBuster. I have some questions regarding the
interpretation of the determined bulk solvent parameters (Ksol and
Bsol). According to the literature, two solvent models are currently
used by different refinement packages: the exponential scaling model
(application of Babinet's principle) and the mask model. According to
Blanc et al., 2004 (PMID: 15572774) it seems that Buster uses
Babinet's principle. In this model Ksol is interpreted as the ratio of
the solvent electron density to the protein electron density, with
average values of 0.75 to 0.95. Bsol limits the contribution of the
solvent to > 5? Angstrom and has values of 150 to 350 A^2.

The values I obtained are: Ksol = 1.032 and Bsol= 155.  Thus it seems
that the average density of the solvent is higher then that of the
protein. Should I be worried about this?
Because of the low resolution most residues are modelled as Ala, and
even some domains are missing (about 20% of the total protein mass in
the asu). I wonder if it is reasonable to state that Ksol is unusually
high because of the unmodelled protein regions? Or is there another
reason for the high Ksol (e.g. chemical composition of the
crystallization solution)?
I also wonder if there is a correlation between Ksol and the
resolution of the data?

Thanks for your input,

best regards,


Kenneth Verstraete
L-ProBE: Laboratory for Protein Biochemistry and Biomolecular engineering
Ghent University
KL Ledeganckstraat 35
9000 Ghent

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