Characterizing the nanostructures of spider major ampullate (dragline) silks is an important step in understanding the origin of their high mean strength and toughness. and for producing polymeric analogs that mimic these properties. Here we present transmission electron microscopy (TEM) diffraction patterns and an accompanying structure factor analysis for the dragline silk of Latrodectus hesperus (black widow spider). The chemical and physical composition of crystalline regions in this silk fiber was studied by manipulating the positions and size of amino acid side groups in a theoretical model, and comparing the expected unit cell scattering amplitudes with experimental electron diffraction patterns. The results suggest that -in addition to the smaller amino acid side groups such as alanine, glycine and serine - some of the bulkier amino acid side groups such as tyrosine and leucine are included in the crystalline fraction of the major ampullate silk. The structure factor analysis also demonstrates a marked sensitivity of the respective diffraction spot intensities to a slight change in both side group position and side group bulkiness. These observations point to a unique function for TEM in characterizing silk and other polymers. (c) 2005 Elsevier Ltd. All rights reserved.