In order to study the unusual thermostability of rubredoxin from Pyrococcus furiosus (RubPf), the structure of a 'triple mutant' of this rubredoxin, which is less thermostable than the wild type, was solved at 1.5-Å resolution by neutron-diffraction analysis using the BIX-3 diffractometer at the JRR-3M reactor of JAERI. The positions of the non-hydrogen atoms are almost the same as the native rubredoxin; however, for Trp3 → Tyr3, large structural changes were found, so that their hydrogen-bonding schemes are significantly different. Some positions of the hydrogen atoms and molecules of hydration are shifted in certain regions, suggesting that such differences may contribute to the differences in thermostability between this 'triple-mutant' rubredoxin and wild-type rubredoxin.