Under gas pressures of 1–3 MPa, xenon can be bound to discrete sites in hydrophobic cavities of protein,so as to use Xe as a heavy atom for determining phases in protein crystallography. Using single anomalous scattering diffraction method, we demonstrate that an interpretable electron density map can be obtained for protein trichosanthin from a single xenon derivative. We found, for the first time, a pre-existing hydrophobic cavity just under the protein surface of trichosanthin.