Lattice nano-ripples revealed in peptide microcrystals by scanning electron nanodiffraction

Changes in lattice structure across sub-regions of protein crystals are challenging to assess when relying on whole crystal measurements. Because of this difficulty, macromolecular structure determination from protein micro and nano crystals requires assumptions of bulk crystallinity and domain block substructure. To evaluate the fidelity of these assumptions in protein nanocrystals we map lattice structure across micron size areas of cryogenically preserved three-dimensional peptide crystals using a nano-focused electron beam. This approach produces diffraction from as few as 1,500 molecules in a crystal, is sensitive to crystal thickness and three-dimensional lattice orientation. Real-space maps reconstructed from unsupervised classification of diffraction patterns across a crystal reveal regions of crystal order/disorder and three-dimensional lattice reorientation on a 20nm scale. The lattice nano-ripples observed in micron-sized macromolecular crystals provide a direct view of their plasticity. Knowledge of these features is a first step to understanding crystalline macromolecular self-assembly and improving the determination of structures from protein nano and microcrystals from single or serial crystal diffraction.