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X-ray photoelectron spectroscopy and electron energy-loss spectroscopy indicate the crystal is Ni deficient. Density functional theory calculations-considering the spatial and electronic disturbance induced by the favourable nickel vacancy-reveal a nanoscale distortion comparable to STM and TEM observations. The different inhomogeneities are understood in terms of the structural relaxation induced by ordering of nickel vacancies, which is predicted to be favourable.The collective behavior of DNA is important for exploring new types of