You did not give much info as to location, number of birds, ect but based on what I read here are some suggestions....
Figure out how many birds you are planning for and multiply that by 4 to give yourself the square footage floor space needed INSIDE the coop. Measure the square footage of your completed run and divide by 10 to see how many birds your run can handle. Go by the SMALLER of the two numbers to see the maximum number of birds you can comfortably house.
A coop is simply a shelter for the birds to roost in. Everything else can be outside if you want as long as it's dry. If your run is secure with skirting, hardware cloth around the lowest part of the run, and a roof or wire top, why not set the coop, raised off the ground so it's chicken usable, inside. Then you don't have security issues and don't have to lock them down every night or get one of those expensive pop doors. Chickens like to be out in all weather, I'm watching mine run around in the rain chasing grass hoppers right now.
A nest box for about every 5 birds (suggest a minimum of two boxes) can be fancy metal or wood set ups, or as simply as a couple recycle bins, cat litter boxes, or milk crates with some straw in them. Feeders can be suspended about chest high inside the coop or outside under a cover to stay dry. Water founts are usually outside to cut down on mess in the coop, especially if you are going to use chips.