The combination of mass spectrometry and single crystal X-ray diffraction of HPLC-purified DNA-stabilized silver nanoclusters (DNA-AgNCs) is a powerful tool to determine the charge and structure of the encapsulated AgNC. Such information is not only relevant to design new DNA-AgNCs with tailored properties, but it is also important for bio-conjugation experiments and is essential for electronic structure calculations. Here, the efforts to determine the structure of a HPLC-purified green emissive DNA-AgNC are presented. Unfortunately, the original DNA-AgNC, known to have four valence electrons, could not be crystallized. By modifying the stabilizing DNA sequence, while maintaining the original spectroscopic properties, several mutants could be successfully crystallized, and for one of them, single crystal X-ray diffraction data provided insight into the silver positions. While the DNA conformation is not resolved, the described approach provides valuable insight into the class of green and dual emissive DNA-AgNCs with four valence electrons. These results constitute a roadmap on how to improve crystallization and crystal quality for X-ray diffraction measurements.