X-ray diffraction was used to monitor the effects of electron microscope fixation, staining, and embedding procedures on the preservation of the three-dimensional crystalline order in collagen fibrils of rat tail tendon. A procedure is described in which the characteristic 3.8-nm lateral spacing is preserved, with increased contrast, in the diffraction pattern ofthe embedded fiber. This spacing is correlated with the separation between the tangentially oriented equally spaced lines of density observed in electron microscope ultrathin fibril cross sections of the same material. Optical diffraction of electron micrographs gives an objective measure of the periodicity and suggests that the fibril is composed of concentrically oriented crystalline domains. These observations, when combined with a recent interpretation of the native x-ray diffraction data [Hulmes, D. J. Nature (London) 282, 878-880] suggest a tentative model for the three-dimensional structure of collagen fibrils.The one-dimensional or axially projected structure of collagen fibrils is well understood, to the resolution of individual amino acids (1-5), in terms of the modified "quarter stagger" theory for the molecular packing (6, 7). However, the way in which this scheme is extended into three dimensions remains controversial (for review, see refs. 8 and 9). X-ray diffraction from tendon fibers (10-12) indicates three-dimensional crystallinity in the molecular packing although, in some specimens, only the onedimensional 67-nm (D) axial periodicity has been observed (13,14). Collagen fibrils are somewhat analogous to liquid crystals (15)(16)(17), and the one-dimensionally ordered and three-dimensionally ordered phases may correspond to a smectic A -) B transition. Several interpretations have been suggested for the near-equatorial (i.e., perpendicular to the fiber axis) crystalline x-ray data (8, 9), but recently both the observed spacings and the general intensity distribution have been accounted for by quasi-hexagonal packing of straight tilted molecules (9, 18). In contrast to most of the tetragonal packing schemes, the quasihexagonal model does not require the presence ofthe rope-like intermediate substructures, a few molecules in cross section, called microfibrils.Electron microscopy, particularly on negatively stained specimens, indicates that collagen fibrils have a filamentous substructure (19,20). Filaments have also been observed during in vitro collagenfibrillogenesis (21-23). Estimates of filament width vary from 1.5 nm to 4 nm, and so it has been suggested that these filaments correspond to either individual molecules (18,19) To date, no concerted attempt has been made to correlate electron microscopic data with the x-ray diffraction observations that indicate three-dimensional crystallinity in collagen fibrils. So far, there has been no evidence from electron microscopy for long-range lateral order in the native molecular packing. In this paper, we describe the initial results of an extensive joint x-ray diffraction-electron ...