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X-rays are produced by excitations of the core level electrons in atoms, and they are useful to detect the type of elements in the periodic table. However, X-ray characterization generally requires a large number of atoms to attain a detectable signal and reducing the size of a sample for X-ray experiments is a long-time goal. To date, X-ray detection of materials can be made on the samples with as few as~ 10 4 atoms due to advances in instrumentation. Here, we show that X-rays can be used to detect metal atoms at the ultimate atomic limit in a quantum tunnelling regime: A single iron atom caged in an organic host, a hexagonal shape supramolecule, has been detected using synchrotron X-ray scanning tunneling microscopy. The experiments were conducted at the XTIP beamline [1] located at the sector 4-ID-E of the Advanced Photon Source of Argonne National Laboratory. Using a specialized coaxial tip …