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The datasheet for the Intel Xeon E3-1230V3 says it supports a maximum of 32GB DDR3-1333/1600. But isn't the RAM speed dependent on whether the motherboard supports it?

I'm thinking of getting this CPU and an ASUS Z87-A motherboard and am trying to decide on the RAM. There's only a small price difference between 16 Gb of 1600MHz vs 2300 MHz so trying to decide if the 2300 is worth the extra £3 or whether it'll cause problems. This is for an Ubuntu-based 3D rendering setup.

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It won’t cause problems. But it won’t run at more than 1600 MHz unless you manually overclock it. Both motherboard and CPU limit maximum speeds. The CPU does because it has the memory controller built-in. The motherboard does because it contains the connection between CPU and memory and needs high-quality components to support high speeds. In your board’s specs you can see the “O.C.” hint—meaning this is a (supported) overclocked speed.

It’s very unlikely you’d benefit from the speed increase anyway.

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