Conversion of the noninfectious, cellular form of the scrapie prion (PrPC) to the infectious form (PrPSc) is thought to be driven by an alpha-helical to beta-sheet conformational transition. The N-truncated polypeptide PrP27-30, which encompasses residues 90-231 of PrPSc and from which the truncated peptide is derived by limited proteolysis, assembles into amyloid rods that are rich in the beta-sheet conformation. The N-terminal half of PrP27-30, which includes residues 90-145 of PrP (SHa90-145) and contains the two putative alpha-helical domains H1 (PrP109-122) and H2 (PrP129-141), appears to be particularly crucial in the alpha --> beta conversion. To assess their role in this conformational transition, we have analyzed in detail X-ray diffraction patterns from the prion-related peptides A8A (PrP113-120), H1, and SHa90-145. We used iterative Fourier synthesis with beta silk as an initial model for assigning phases. For H1, the lyophilized and acetonitrile-solubilized/dehydrated specimens gave two different electron density maps. The former showed that the beta-sheets were composed of small side chains as in A8A. The latter showed two types of beta-sheets having smaller and larger side chains, suggesting a turn. Such a turn was not observed in the lyophilized H1, indicating that the internal turn in H1 depends on the physical-chemical environment. In SHa90-145, the beta-chains are assembled in similar to 40 Angstrom-wide crystal domains (termed beta-crystallites), and the electron density maps of these crystallites showed evidence for turns within both the H1 and H2 domains. The molecular folding of H1-H2 is compared here with the recent NMR solution structure of recombinant hamster prion, and the effect of pH on the conformational change is discussed. The most compact structure based on the X-ray diffraction analysis showed that the N-terminal, smaller residues of H2 fold back and are hydrogen-bonded with the C-terminal, smaller residues of H1. Similar folding is observed in the NMR solution structure. Comparison of the NMR structures at different pH with the X-ray diffraction results suggests that histidine and lysine residues in the N-terminal sequence of PrP may figure in the alpha --> beta structure transition of PrP.