Im sorry.
Probably the easiest way to protect them is to create a door to your coop and shut them away at night and let them back out in the morning.
What is the run made of?? The only wire I would trust completely to leave out at night is hardware cloth or a combo of welded wire and chicken wire.
You can wire the floor, if will be okay on their feet, but what is your run roof made of? Most predators will climb right over the top. You can do the curtain of wire where you lay it outside the run on the ground. Be sure that is where the aniaml got in though or your efforts will be a complete waste.
Again, sorry about your chickens. We have almost all lost one or two to predators over the years, it stinks.
Oh and be sure to take care of them closely tonight, whatever it is will be back most night for a while looking for more.