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I'm building a machine based on the Econobox and I was wondering if it is worth it to upgrade to a P45 based motherboard. Is the only difference between the P35 and P45 PCI Express 2.0? Will I really notice the difference between old PCIe and PCIe 2.0?

In a nutshell,

P35= 90nm, dual-channel DDR2, optional DDR3 support, PCIe 1.1 support, Official 333/1333Mhz FSB support.

P45 = 65nm, dual-channel DDR2, optional DDR3 support, PCIe 2.0 support, Official 400/1600Mhz FSB support.

With a single card, most likely not- in Crossfire (with 4000 series I hope) it's been measured. But if you're going cheap, a single 4850 is plenty and would work great with P35.

If you can afford the $30 difference, then why not. If you really are running tight in the budget, the P35 is good enough and well-proven.