This area is filled with Super Mutant Overlords so you may be in a long firefight before you can clear it out. The shop in front of the scrapyard has an Advanced safe and ammo box.
In the middle of the scrapyard is a wooden shack. Make your way to the topmost shack to find a steamer trunk, supermutant arm guards, mini-nuke inside the fridge, and an issue of Tales of a Junktown Jerky Vendor.
Near that shack is a flipped blue train. Climb on top of it to find the shelter door. It’s sealed tight so trace the black cable to find the circuit breaker. Activate it to open the shelter door. The safe has a railway rifle, some Aluminum cans, and Big John’s Safe Key. The Master safe is located in the nearby house, on the second floor beside the terminal. Use the key to open the safe.