Plural subject and singular predicate

• ？ Graphs are a special data structure.

It's grammatical, but it doesn't parse very well.

Consider this:

• ✔ Apples are a joy to eat.

The problem with the particular sentence in the question is that it's unexpected. Even though the syntax is valid, it's not what we'd expect to hear, because on first glance it appears to confuse a plurality with a singularity (although it actually doesn't). As such, it's slightly unidiomatic.

One variation that sounds better simply inserts two words:

• Graphs are a special kind of data structure.

Other variations replace the verb:

• Graphs belong to a special data structure.
• Graphs share a special data structure.