Can I use a [6Gbits/sec SATA-3] drive in a 2009 Mac-Pro
Executive summary: Most regular commercially-available drives you buy new today will install and work fine. It IS worthwhile to pay extra for a drive with a bigger buffer, but do not pay EXTRA for SATA-3 alone, it is all specsmanship.
If you buy a weird older drive, or you have a really old Mac, it may not work properly. [WD Raptors and VelociRaptors work fine.]
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RE: SATA Bus speed:
Rotating drives available today, whatever their SATA spec, can source data off the spinning platters no faster than about 125MBytes/sec.
SATA 3 is rated at 6G bits/sec, which theoretically is about 750 Mega Bytes/sec
SATA 2 is rated at 3G bits/sec, which is theoretically about 375 Mega Bytes/sec
SATA 1 is rated at 1.5G bits/sec, which is theoretically about 187.5 Meg Bytes/sec
None of the SATA Busses is a bottleneck for consumer Rotating drives you can buy today. Trying to speed up the SATA Bus will not provide any real-world performance increases for Rotating Drives.
Even most common SSD drives are not bottlenecked by SATA 2.
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If you put the drives on a PCIe card, they are not bottlenecked by the SATA on the card either, as it will typically be SATA 3.
But unless you have the very fastest SATA drives available, you are in no danger of having the existing main SATA 2 Bus in your Mac Pro slow you down. The card is only needed for the fastest SSD drives available today, and will not provide much current speed improvement even in that case.