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Is it possible to run a system with Shuttle PSU and non Shuttle motherboard?

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There isn't a set standard for Mini-ITX boards (http://en.wikipedia.org/wiki/Mini-ITX), and I've not seen many ITX power supplies, but the ITX boards I've looked at all seem to share a common standard, so you should be OK. I'd also make sure to check the power supply matches the voltage, current and frequency, or get a unit that is labelled "Full Range" or equivalent.

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Assuming it has the correct number of pins (20/24) and the necessary power outputs you need (Sata/molex/PCI-E(Video)) it should work. Its impossible to tell without details on both the parts in question. You could, in theory use a mini itx motherboard with a standard PSU and vice versa, so it SHOULD be possible unless shuttle uses a non standard power input of some sort.

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