The following information is about the train shown in the movie.
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, 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 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.
Aside from the Alien, the train was loaded with various military cargo. The refrigerated boxcars were loaded with frozen meats (Most likely food for the alien.) of various kinds (Seen on the manifest clipboard plus scattered throughout the wreckage in the Portal 2 Interactive). The tank cars were carrying flammable liquids (Most Likely aviation fuel, or related liquid). While the containers on the flat cars, and standard boxcars carried military equipment plus alien related research material.
- 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 railroad the train wrecks on is owned by the Grand Ohio Railroad. (As seen on some posters, and stickers on the depot walls.) (The Grand Ohio is a fictional railroad created for the movie.).
- 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.