This program calculates normalized
probabilities for the occurrence of multimerization states based on a recent
survey (Nov. 2002) of the Vm (Matthews coefficient) and solvent content (Vs) distribution of about 11,000
non-redundant crystallographic PDB entries (Kantardjieff and Rupp,
Higher packing density and this lower solvent
content significantly correlate with increasing resolution and can be used to provide a more
refined probability for the occurrence of a certain oligomerization state. The
program thus accepts
resolution as additional information to select the proper probability distribution.
is that observed resolution represents an estimate for the lower limit for crystal quality, i.e.,
crystals obviously diffract to at least this value (but could also diffract better).
It must be understood that the answers are always relative probabilities based
on our current state of knowledge and that no clear answer may result in certain
One can also enter the molecular data for
one monomer and select its known multimerization state, in case you know what
basic multimer unit you are looking for. For example, if your known molecular unit is a trimer, you may
want to look for 3-mer, 6-mer, 9-mer etc. Note that crystallographic axes coinciding with multimer axes can result in improbably
low Vm for a single multimer unit.
The results are represented in
tabular form at the top of the output followed by two graphs showing the
normalized probability distributions (resolution corrected and all PDB data) against Vm and Vs, respectively.
We would appreciate citation of the
two following references when using this program in published work:
Matthews BW. 1968. Solvent content of
protein crystals. J Mol Biol 33:491-497.
Kantardjieff KA, Rupp B. Matthews
coefficient probabilities: Improved estimates for unit cell contents of
proteins, DNA, and protein-nucleic acid complex crystals.
endnote format (ps.enl) here. The
fit function and
parameter files are also available for download.