A non-camelized human V-H domain has been crystallized through limited in vitro proteolysis of scFvM12 antibody fragment. The protease addition results in the complete degradation of the M12-V-L domain, linker, and purification tags. The structure solved up to 1.5 angstrom resolution having good stereochemistry with a R-cryst factor of 15.8% and R-free factor of 19.7%. Dihedral angle values comparison of the first and the second complementarity-determining region (CDR) of M12-V-H domain with an average values show a significant deviation; therefore, M12-V-H domain structure indicates either the existence of a new canonical subclass or a link among the subclasses of canonical main-chain conformation in V,3 family. The presence of uncommon hydrogen bond between Ser-H50 and Tyr-H97 has pulling effect on CDR-H3 loop. The interface area buried by CDR-H3 loop indicates the partial coverage of the hydrophobic V-L-V-H interface. The isolated M12-V-H domain was found soluble up to 0.35 mM. This result would be helpful in structure based designing of an isolated human single domain antibody fragments for biotechnological and pharmaceutical applications such as cancer. (C) 2005 Elsevier Inc. All rights reserved.