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danny,
molecular bio isn't my field, so take this for what its worth.
you know the mass of the (single?) protein in Daltons. You know the density, therefore you know the volume. if you assume a spherical approximation, wouldn't this give you a radius?
I can see using the properties of water if you don't know the number of protein molecules in the 5000 Da sample; then you assume that you have the same number of molecules in the volume you calculate for the protein as you would in a the same volume of water, as you already know the density and molecular weight of water at 20 deg C.
That's my quick and nasty, at least.
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