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Among the reactions involved in the production and destruction of deuterium during Big Bang Nucleosynthesis, the deuterium-burning D(p,gamma)3He reaction has the largest uncertainty and limits the precision of theoretical estimates of primordial deuterium abundance. Here we report the results of a careful commissioning of the experimental setup used to measure the cross-section of the D(p,gamma)3He reaction at the Laboratory for Underground Nuclear Astrophysics of the Gran Sasso Laboratory (Italy). The commissioning was aimed at minimising all sources of systematic uncertainty in the measured cross sections. The overall systematic error achieved (<3 %) will enable improved predictions of BBN deuterium abundance.