The difference between PCI Express 2.0 x16 and PCI Express 2.1 x16 is that version 2.1 supports the new protocol options found in PCI Express 3.0 while version 2.0 does not. The two versions don't have any compatibility issues with each other. Using a motherboard with one version number that doesn't match the other is not cause for alarm. Additionally, the x16 designation is typically associated with graphics cards.
According to RTC, a computing magazine, the PCI Express 2.1 designation adds the new transaction layer features present in the PCI Express 3.0 standard to the 2.x standard. These new features equate to better power management and reduced power consumption by the PCI Express connected device. RTC says the 2.1 revision was created with the new 3.0 features because the new features are not contingent on the increased bandwidth found in version 3.0.
The PCI Express standard is backward and forward compatible, meaning that any card that supports that standard regardless of version number will work with any motherboard that supports the standard. According to PCI SIG, an organization for PCI standards, a version 1.1 supporting motherboard will work with a version 3.0 card and vice-versa. However, motherboards can have power management related manufacturing defects that cause cross-version compatibility problems with cards. It's possible that the power consumption difference from a 2.1 card on a 2.1 motherboard could work, while a 2.0 card on the same board might not because the computer power supply doesn't have sufficient wattage. However, a computer that has enough power to run a card on the 2.0 standard should have minimal problems running a card at the 2.1 standard and vice-versa.
The "x" number on the PCI Express slot or card indicates how many data lanes it uses and is different from the version number. A PCI Express 2.1 x16 device and a PCI Express 2.0 x16 device use the same size connection. Other PCI Express 2.x devices use a x1, x2, x4, or x8 connection, which indicates how many data lanes they use. The number of lanes effects both the size of the connection on the card and the motherboard slot as well as the maximum bandwidth the two can use to communicate. An x16 card uses twice the bandwidth of an x8 card.
The 2.0 and 2.1 version numbers signify the most important difference between 2.0 and 2.1. While the 2.1 version doesn't run any faster than the 2.0 version, it features new protocols. When it comes to performance and rare compatibility issues over power management, the first digit is the relevant one. A 2.x PCI Express card has twice the bandwidth of a 1.x PCI Express card that uses the same number of lanes. Additionally, the 3.x standard has twice as much bandwidth as the 2.0 version. The performance difference when comparing the 2.0 and 2.1 versions is negligible.
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