Filamentous bacteriophage (phage) are single-stranded DNA viruses that infect bacteria. Single-site mutants of fd phage have been studied by magic-angle spinning nuclear magnetic resonance and by small-angle X-ray scattering. Detailed analysis has been performed that provides insight into structural variations on three length scales. The results, analyzed in conjunction with existing literature data, suggest that a single charge mutation on the capsid surface affects direct interviral interactions but not the structure of individual particles or the macroscale organization. On the other hand, a single hydrophobic mutation located at the hydrophobic interface that stabilizes capsid assembly alters the atomic structure of the phage, mainly affecting intersubunit interactions, affects its macroscale organization, that is, the pitch of the cholesteric liquid crystal formed by the particles, but skips the nanoscale hence does not affect direct interparticle interactions. An X-ray scattering under osmotic pressure assay provides the effective linear charge density of the phage and we obtain values of 0.6 Å-1 and 0.4 Å-1 for fd and M13 phage, respectively. These values agree with a simple consideration of a single cylinder with protein and DNA charges spread according to the most recent atomic-resolution models of the phage.