Througout many of the episodes, Scully's apartment numbers are usually in the higher numbered range (I've seen it in the 400's). However, in "Duane Barry," Scully was kidnapped through her ground floor window.
actually in the majority of the episodes, mulder's apartment number is 42 and scully's is 5. it does change a lot (a lot of the hotel numbers are higher, and sometimes her apartment number even changes) but usually her number is 5.
It is also worth noting that the number of the apartment opposite Mulder's is 23. The numbers 5, 23 and 42 are very popular among sci-fi fans, as the two former plays important role in "Illuminatus!" trilogy by R.A.Wilson and R.Shea, and the latter is a joke from D. Adams' "The Hitch-Hikers Guide to Galaxy". So, as the in-movie jokes and references, they don't need to exactly refer to actual numbering convention.