If the OP is using
http://www.dofmaster.com/dofjs.html as his DOF calculator, then it's already taken into account the difference in the CoC's between the two formats.
Edit: I don't know what he's using, but in
http://www.dofmaster.com/dofjs.html, the 4x5 calculations for f64 are right, but the 6x6(?) calculation for f/22 are different--the markings on his lens aren't quite accurate to the caculator...
Additionally: for both formats, focusing at 50ft is unnecessary since the hyperfocal distance is much closer than that. If you open up a 4x5 lens to f/32, you can focus at 23.6ft and get everything in focus from 11.8ft to infinity.
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