Bioluminescence scientists have determined the crystal structure of the wild-type luciferase from a Japanese firefly in complex with an analog of the high-energy reaction intermediate. They have also solved the structure of a mutant luciferase emitting red light in complex with the same compound. A comparison of these structures reveals that the hydrophobicity and the rigidity of the protein surrounding oxyluciferin are important for the color of the emitted light. Understanding how the color of the emitted light alters with changes in the luciferase sequence may allow for the engineering of new molecules useful for biological experiments.