Synchrotron X-ray diffraction was applied to study the structure of biogenic α-chitin crystals composing the tendon of the spider Cupiennius salei. Measurements were carried out on pristine chitin crystals stabilized by proteins and water, as well as after their deproteinization and dehydration. We found substantial shifts (up to δq/q = 9% in the wave vector in q-space) in the (0 2 0) diffraction peak position between intact and purified chitin samples. However, chitin lattice parameters extracted from the set of reflections (hkl), which did not contain the (0 2 0)-reflection, showed no systematic variation between the pristine and the processed samples. The observed shifts in the (0 2 0) peak position are discussed in terms of the ordering-induced modulation of the protein and water electron density near the surface of the ultra-thin chitin fibrils due to strong protein/chitin and water/chitin interactions. The extracted modulation periods can be used as a quantitative parameter characterizing the interaction length.