Molecular reactions involving proteins take place at a variety of hierarchical spatial levels, ranging from Å to sub-μm scales, e.g., local chemical reactions inside protein molecules, tertiary structural changes of whole molecules, and association-and-dissociation of ensembles of multiple molecules. Because of the absence of techniques to observe all of these reactions coincidentally, it is important to choose an adequate method for investigating the molecular events occurring at each level of the spatial hierarchy. In this paper, I describe the tertiary structural changes and the local structure of hydrogen bonding network of the light-sensor protein, photoactive yellow protein (PYP), investigated by neutron/X-ray joint crystallography and wild-angle solution scattering experiments, respectively. Furthermore, based on these results, the interdependency among the molecular events at the different spatial hierarchies will be discussed.