Single-particle analysis (SPA) by X-ray free electron laser (XFEL) is a novel method that can observe biomolecules and living tissue that are difficult to crystallize in a state close to nature. To reconstruct three-dimensional (3D) molecular structure from two-dimensional (2D) XFEL diffraction patterns, we have to estimate the incident beam angle to the molecule for each pattern to assemble the 3D-diffraction intensity distribution using interpolation, and retrieve the phase information. In this study, we investigated the optimal parameter sets to assemble the 3D-diffraction intensity distribution from simulated 2D-diffraction patterns of ribosome. In particular, we examined how the parameters need to be adjusted for diffraction patterns with different binning sizes and beam intensities to obtain the highest resolution of molecular structure phase retrieved from the 3D-diffraction intensity. We found that resolution of restored molecular structure is sensitive to the interpolation parameters. Using the optimal parameter set, a linear oversampling ratio of around four is found to be sufficient for correct angle estimation and phase retrieval from the diffraction patterns of SPA by XFEL.