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The data presented in this article are related to the research article entitled Structure of Self-assembled Native Soy Globulin in Aqueous Solution as a Function of the Concentration and the pH by N. Chen, M. Zhao C. Chassenieux, T. Nicolai (2016) [1]. Please refer to this article for interpretation of the data. The protein composition of soy protein isolate (SPI) was characterized by SDS-Page. The molar mass of native soy globulin aggregates formed at different protein concentrations was determined by light scattering as a function of the waiting time. The dependence of the pH on the net charge density of native soy globulins was determined for solutions containing 5 g/L or 2 g/L SPI.