A commonly adopted model for the microstructure of Nephila clavipes major ampullate silk (MAS) is similar to that used for Bombyx mori (silkworm) silk: a simple composite wherein discrete, essentially perfect crystals are dispersed throughout an amorphous protein matrix. However, inconsistencies arise when researchers using complementary microstructural characterisation techniques attempt to explain their results within that framework. We present here the findings of our parallel studies in x-ray diffraction, electron microscopy, and molecular modeling. These results, combined with other data gleaned from the literature, lead us to propose a revised description of the spider silk microstructure. The new model recognizes that the 70-500 nm sized ordered regions in MAS cannot be constructed from a simple motif of repeating monomers, and develops the concept of non-periodic lattice (NPL) crystals to characterize these structures. The local composition, symmetry, and perfection of order vary over distances that are small compared to the size of an NPL crystal.