F1-ATPase is a rotary molecular motor driven by ATP hydrolysis that rotates the ␥-subunit against the ␣33 ring. The crystal structures of F1, which provide the structural basis for the catalysis mechanism, have shown essentially 1 stable conformational state. In contrast, single-molecule studies have revealed that F1 has 2 stable conformational states: ATP-binding dwell state and catalytic dwell state. Although structural and single-molecule studies are crucial for the understanding of the molecular mechanism of F1, it remains unclear as to which catalytic state the crystal structure represents. To address this issue, we introduced cysteine residues at E391 and ␥R84 of F1 from thermophilic Bacillus PS3. In the crystal structures of the mitochondrial F1, the corresponding residues in the ADPbound  (DP) and ␥ were in direct contact. The E190D mutation was additionally introduced into the  to slow ATP hydrolysis. By incorporating a single copy of the mutant -subunit, the chimera F1, ␣32(E190D/E391C)␥(R84C), was prepared. In single-molecule rotation assay, chimera F1 showed a catalytic dwell pause in every turn because of the slowed ATP hydrolysis of (E190D/E391C). When the mutant  and ␥ were cross-linked through a disulfide bond between E391C and ␥R84C, F1 paused the rotation at the catalytic dwell angle of (E190D/E391C), indicating that the crystal structure represents the catalytic dwell state and that DP is the catalytically active form. The former point was again confirmed in experiments where F1 rotation was inhibited by adenosine-5-(,␥-imino)-triphosphate and/or azide, the most commonly used inhibitors for the crystallization of F1. ATP synthase ͉ cross-link