Theory is that the height of all of the strings at the nut should be the same as the plane of the frets. In practice, some people like to allow a few thousandths of an inch more than that and to vary that amount by a few thousands of an inch from bass strings to treble strings.
If the "rattle" sound you have is due to the A and D strings being too low at the nut, those two slots can be filled with CA glue and baking soda or bone dust and then recut to the correct depth. (The symptom of a nut slot being too low is that the open string buzzes or rattles on the first fret.) Alternatively, one can shim the entire nut and recut all of the slots to the correct depths. Or, one can simply replace the nut and cut each slot to its correct depth.
One method that I like is to use a stack of feeler gauges that total the height of the first fret - or a few thousandths more. One then cuts/files to the top of the feeler gauges with the stack of gauges adjacent to the nut.
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