The spatial structure of dimeric green fluorescent protein EGFP-K162Q with MDELYK (EGFPv) C-terminal deletion has been assigned in the P61space group with resolution 1.34 Å by X-ray diffraction analysis. The results have been compared with X-ray diffraction data of monomeric EGFP (green biomarker with enhanced photophysical properties) assigned in another crystal space group, P212121, with resolution 1.50 and 1.35 Å. Subunits in the EGFPv dimeric structure are located at 75° angle with the contact area 800 Å2. The dimeric framework is stabilized by the six hydrogen bonds and central hydrophobic core of six residues. The root-mean-square deviation value for Cαatoms in 3-230 residues of the P61and P212121crystal structures is 0.55 Å. The differential characteristics of EGFPv-P61structure, compared to that of P212121, is a noticeably different orientation of the Glu222 side chain, and a new conformation of the 155-159 loop fragment, characterized by deviations among the Cαatoms of superimposed structures reaching 4.6 Å for Lys156 and 5.5 Å for Lys158. © 2014 Pleiades Publishing, Ltd.