Well I used 50x50x3 and 100x50x3 albeit on a smaller machine. These sizes were ideal and provided the design is right there should be no flexing of the structure. You do though have to consider that the 3mm thickness is not much if you intend making threaded holes in it, and you will for the X rails at least. In my case I glued a piece of 30x6 flat strap inside to beef the threaded thickness to 9mm.
I think you should go with the 5mm thickness