Stone deepest of all, also in empty box (4)
I believe the answer is:
onyx
'stone' is the definition.
(type of gemstone)
'deepest of all also in empty box' is the wordplay.
I cannot quite see how this works, but
'of' could be 'o' and 'o' is present in the answer.
The remaining letters 'nyx' is a valid word which might be clued in a way I don't understand.
This explanation may well be incorrect...
Can you help me to learn more?
(Other definitions for onyx that I've seen before include "Black variety of quartz" , "Semi-precious variety of agate" , "Chalcedony agate" , "Hard stone with coloured layers" , "Form of chalcedony" .)