We propose a new algorithm based on the scattering pattern matrix and the maximum entropy method to achieve a very precise investigation of the three-dimensional atomic nucleus positions in material by the electron holography technique. The forward scattering problems, i.e. strong intensity of forward focusing peak, and frequency shift in the forward scattering region, are solved in this algorithm, since the forward scattering effects are almost perfectly taken into account. We applied the algorithm to an experimental single-energy hologram of Si 2s photoemission with kinetic energy Ek = 1110.3 eV from a Si(001) single-crystal surface and succeeded in reconstructing the atomic nucleus positions of the Si bulk structure. The reconstructed space size is about 800 picometers, and as many as 21 atoms are recognized. The accuracy of the position for most atoms is within 50 picometers.