Real-space quantum-based refinement for cryo-EM: Q|R#3

Electron cryo-microscopy (cryo-EM) is fast becoming a major competitor to X-ray crystallography especially for large structures that are difficult or impossible to crystallize. While recent spectacular technology improvements are leading to significantly higher resolution of three-dimensional reconstructions, the average quality of cryo-EM maps is still on the low-resolution end of the range compared to crystallography. A long-standing challenge for atomic model refinement has been the production of stereochemically meaningful models for this resolution regime. Here we demonstrate how including accurate model geometry restraints derived from ab initio quantum-chemical calculations (HF-D3/6-31G) can improve the refinements of an example structure (chain A of 3j63). The robustness of the procedure is tested for additional structures with up to 7k atoms (3a5x, and chain C of 5fn5) by means of the less expensive semi-empirical (GFN1-xTB) model. Necessary algorithms enabling real-space quantum refinement are implemented in the latest version of qr.refine and are described herein.