An application of angular X-ray cross-correlation analysis (AXCCA) to the scattered intensity distribution measured in 3D reciprocal space from a single-crystalline sample is proposed in this work. Contrary to the conventional application of AXCCA, when averaging over many 2D diffraction patterns collected from different randomly oriented samples is required, the proposed approach provides an insight into the structure of a single specimen. This is particularly useful in studies of defect-rich samples that are unlikely to have the same structure. The application of the method is shown on an example of a qualitative structure determination of a colloidal crystal from simulated as well as experimentally measured 3D scattered intensity distributions.