MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.

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Mine lets you use 3mm screws in the slot no problem. Are you guessing or have you actually tried it?
Also, don't reuse the OEM screws on the lock, get new 3mm screws for that.