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Calculation of resolution dependent Matthews Probabilities

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, Protein Science 12:1865-1871, 2003).

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. The assumption 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 cases.

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. Protein Science 12:1865-1871 (2003)

References in endnote format (ps.enl) here. The fit function and parameter files are also available for download.

 Unit cell a b c (Å) al be ga (deg)

Sample type:

Data resolution: (Useful range 1.2Å - 3.5Å, only used for proteins)

Basic multimer unit:

Spacegroup or spacegroup number: (List of allowed SG symbols)

Select molecular weight option: is