Using the atomic force microscope (AFM) in-situ during the crystallization of a model protein, we investigate the elementary processes of crystal growth at the molecular level. We show that the density of the incorporation sites (kinks) on growth steps propagating on the surface (i) is the same as at equilibrium, and (ii) does not depend on the macroscopic step orientation since during growth the steps consist of segments along the dense crystallographic directions. Observation (i) allows evaluation of the bond energy between molecules in the crystal as 3.2 k(B)T. Furthermore, we determine the frequency of attachment of molecules at the kinks and show that step motion is fully described by this frequency and the kink density. We monitor the formation of point defects and show that, unlike in semiconductors, they are caused by incorporation of impurity particles and therefore are nonequilibrial. The point defects replicate in subsequent layers due to the strain they cause. We demonstrate that using single-molecule manipulation with the AFM tip the defects can be "healed" to restore the regular lattice.