The train

The following information is about the train shown in the movie.

The Locomotive

The U.S. Air Force locomotive involved in the wreck / derailment was a Baldwin S-12. The locomotive's number was #1912  (As seen on a manifest paper in the Portal 2 Interactive trailer). The USAF never had an S-12 numbered 1912, though locomotives of this type was used by the Air Force. USAF #1864 is a good example.

The Rolling Stock

The rolling stock is a mixture of boxcars (Some were refrigerated), tank cars, intermodal flat cars with containers (As seen in the wreck clean up), and military mobile command cars. The boxcars were a mix of standard 50 foot freight type (Like this), and specially designed cars based on Amtrak material handling cars (Like the one the Alien busted out of).

The military mobile command cars (Exterior briefly seen in the first trailer, interior seen in the interactive trailer.) are based on Ex-troop kitchen / sleeper cars used in WWII to carry military personnel (Based on the window arrangements). The cars in the movie had been converted into mobile command / guard centers. Though some could have been used for their original purpose.

The Cargo

Aside from the Alien, the train was seen carrying military computers (Seen briefly in the first trailer) along with frozen meats of various kinds (Seen on the manifest clipboard plus scattered throughout the wreckage in the Portal 2 Interactive). The tank cars in the train were carrying some sorts of flammable liquids (most Likely aviation fuel, or related liquid). While the containers on the flat cars carried military equipment, and alien related research material.

Trivia

• The route the train would have taken in real life would have used at least 4 different railroad's lines: Southern Pacific, Union Pacific, Chicago Rock Island & Pacific, and Conrail.  (Map from the movie), however the line the train wrecks on seems to be owned by a railroad known as the "Grand Ohio Railroad" (As seen on some posters and stickers on the train station).
• Area 51 has no direct rail access. The closest railroad is the Union Pacific in Las Vegas. According to the map, everything was trucked north to (What looks to be) Battle Mountain, NV instead.
• Though very rare, a car can derail a train, but not in the catastrophic fashion shown in the movie.
• According to the screenplay, the train consists of 82 cars.
  • Additionally, the train appears to be going way above it's top speed, not to mention horsepower.