I know the guy who set the question on this elective two years in a row...
Mass defect questions will always and only be based on the mass of the nucleus - sorry to earlier responders - so if you are given the mass of Helium-3 nucleus as 3.0160293 amu and the mass of a proton as 1.00727647 amu and the mass of a neutron as 1.008664 amu, then the mass defect is the difference between the mass of the He-3 nucleus and the masses of two protons and two neutrons i.e. 3.0160293 - (2 x 1.00727647 + 1.008664) = -0.007188 amu. Please note that the total mass of the individual protons and neutrons is higher than the mass of the He-3. This difference is due to the binding energy that is needed to hold the He-3 nucleus together.