S.-T. Yau* and Peter G. Vekilov*†

*Center for Microgravity and Materials Research, and †Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA

The structure of the nucleus largely determines the thermodynamics and kinetics of first-order phase transitions . A compact three-dimensional arrangement of the molecules in the nucleus has often been assumed . Recent molecular dynamics simulations predict a compact nucleus structure for atoms or molecules with a spherical interaction field , while strongly anisotropic, dipolar molecules may bear nuclei consisting of a single chain of molecules . Here, using atomic force microscopy (AFM) in situ during the crystallisation of the protein apoferritin, we image the arrangement of the molecules in near-critical clusters, larger or smaller than the crystal nucleus, that are representative of its structure. In the supersaturation Dm/kBT range of 1.1–1.6, the nuclei contain 50–20 molecules. Within the nuclei, the molecules are arranged as in a large crystal. Contrary to the general belief, the nuclei are not compact molecular assemblies, but are planar arrays of about 5-10 rods of 5-7 molecules set in one or two monomolecular layers. Similarly unexpected nuclei structures might be common, especially for anisotropic molecules. Hence, the nucleus structure should be considered as a variable by advanced theoretical treatments.