by Peter Nollert
November 27, 2009 15:44
When it comes to the design of optimization matrices, think 12, 4 or and 3. But NOT 10.
Here is why: Crystallization plates come in 3x4, 4x6, 8x12, 16x24 formats, not 10x10. I don't know what's the underlying reason for this non-metricity, but I suspect it may be related to the finding that the width of modern railroad tracks is based on history extending back to Roman (apparently it's not). Somehow we're stuck with this somewhat unwieldy dozenal (or is it duodecimal, or duodenary?) system.
Regardless, the protein crystallization plates we're dealing with are rectangular and typically have 24, 96 or 384 wells. Therefore designing crystallization matrices for such 4x6, 8x12 formats makes a lot of sense because they nicely fit into thes plates. When I start with an optimization matrix I usually pick the minimum and maximum concentration and then fill in the concentration for the remaining wells. The practical consequence is that for 96 well plates the numbers 11 and 7 assume a special meaning since those are the divisors used when calculating all concentrations in the well. Dividing by 12 or 8 does not give you equally spaced values because you're boxing in conditions 1 to 12 and there's not well zero.
Multipliers for columns and rows to design protein crystallization gradient matrices that nicely fit a 8 x 12 screen into a standard 96 well protein crystallization plate.
If that's too much of a pain, I'd recommend checking out the E-screen builder. It does all of this on the fly and much more. Check it out.
Happy Thanksgiving,
Peter