Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality.

Here, we determine the 3D coordinates of 6,569 Fe and 16,627 Pt atoms in an FePt nanoparticle with 22 pm precision. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries and point defects. We show that experimentally measured 3D atomic coordinates can be used as direct input for DFT and MD calculations of material properties. This work makes significant advances in characterization capabilities and expands our fundamental understanding of structure-property relationships, which we expect to find applications in physics, chemistry, materials science, nanoscience and nanotechnology.