Mac Pro (Original) and Mac Pro (8x)
The Mac Pro features four PCI Express 16-"lane" connectors on the main logic board. In PCI Express, these are known as "x16" slots. These can be used for PCI Express-compatible cards, like the ATI Radeon card that is available as a configure-to-order option in the Mac Pro.
PCI Express cards will work in slots that are at least as large as the card is. This means that the "x16" slots in the Mac Pro computer also supports "x1" and "x4" cards as well. However, all four slots cannot simultaneously support four cards that implement the same lane configuration. Only one slot actually has 16 lanes going to it—you can put a x16 card into a slot that is only using one lane and it will operate properly, but it will operate more slowly than the same card in a x4, x8 or x16 slot.
With the Expansion Slot Utility, located in /System/Library/Core Services, you can configure the number of lanes available in each slot of a Mac Pro (Original) or Mac Pro (8x), as illustrated below. This example shows a "x16" graphics card occupying the first slot, and the other slots are configured to support an "x1" card in slot two and "x4" cards in slots three and four. The example shows the other options available. When you have picked the appropriate configuration of slots to support your compliment of PCI Express cards, click the Save and Restart... button to implement the configuration.
Note: If you see an "Expansion Slot Utility is not intended to run on this system" message, the lanes are set in a default configuration and cannot be modified.
Mac Pro (Early 2008)
The Mac Pro (Early 2008) computers implement PCI Express revision 2.0 which support twice the data rate per lane as the PCI Express revision 1. Slots 1 and 2 are both x16 revision 2.0 slots. Slots 3 and 4 are both x4 revision 1 slots. Placing a revision 1 card in a revision 2.0 slot, or visa-versa, is supported and results in a revision 1 link.
The number of lanes for each of these slots is permanently set for the Mac Pro (Early 2008). The Expansion Slot Utility doesn't apply.
Mac Pro (Early 2009), Mac Pro (Mid 2010), and Mac Pro (Mid 2012)
The Mac Pro (Early 2009), Mac Pro (Mid 2010), and Mac Pro (Mid 2012) computers implement PCI Express revision 2.0 for all four slots. Slots 1 and 2 are x16 slots, and slots 3 and 4 are x4 slots. As with the Mac Pro (Early 2008), placing a revision 1 card in a revision 2.0 slot works and results in a revision 1 link.
The Expansion Slot Utility is not required for these configurations, since the number of lanes for each slot are permanently set.