An atomically resolved gold nanocluster Au99(C≡CC6H3-2,4-F2)40 (Au99) with an unusual 59 valence electrons has been synthesized. Single-crystal X-ray diffraction reveals that its Au79 kernel is a Au49 Marks decahedron capped by two Au15 units. The surface structure of Au99 consists of 20 linear Au(C≡CR)2 staples. Intercluster interactions are observed between these D5 symmetric clusters. The existence of an unpaired electron is verified by magnetic measurement. Interestingly, this open-shell gold cluster Au99 stays intact in toluene solution at 80 °C for more than a week, and it has good charging-discharging capability under electrochemical conditions. The compact ligand shell protection around the symmetric core accounts for the high stability. This work suggests that geometric factors may play a crucial role in determining the stability of a metal nanocluster, even though the cluster has an open-shell electronic structure.