Extensive molecular dynamics simulations of xenon in two classes of zeolite crystal systems, one consisting of purely intra-crystalline space and the other with both intra- and inter-crystalline space are reported. The latter mimics a typical poly-crystalline sample of zeolite. Comparison of results from these two systems provides insights into the structure and dynamics in the presence of inter-crystalline space. The temperature, as well as the distance between the crystallites, has been varied. The density distribution and diffusivities calculated inside the poly-crystalline system show that the interfacial region between the crystal and the inter-crystalline region acts as a bottleneck for diffusion through the system. At lower temperatures, the particles are trapped at the interface due to the pronounced energy minima present in that region. With the increase in temperature, the particles are able to overcome this barrier frequently, and the transport across the inter-crystalline region is increased. A ballistic or superdiffusive motion is seen in the inter-crystalline region along all the axes except along the axis which has the inter-crystalline space. The transition time for ballistic to diffusive motion increases with the increase in the length of the inter-crystalline space. Velocity auto- and cross correlation functions exhibit strong oscillations and exchange of kinetic energy along directions perpendicular to the direction of the inter-crystalline space. These results explain why uptake and PFG-NMR measurements exhibit lower values for diffusivity for the same system when compared to Quasi-Elastic Neutron Scattering. Thus, using molecular dynamics simulations, we were able to correlate the difference of diffusivity values measured using various experimental methods where these inter-crystalline regions are common.