Cryo-EM single particle structure refinement and map calculation using Servalcat

Abstract

In 2020, cryo-EM single particle analysis achieved true atomic resolution, thanks to technological developments in hardware and software. The number of high resolution reconstructions continues to grow, increasing the importance of accurate determination of atomic coordinates. Here, a new Python package and program called Servalcat is presented that is designed to facilitate atomic model refinement. Servalcat implements a refinement pipeline, using the program REFMAC5 from the CCP4 package. After the refinement, Servalcat calculates a weighted Fo − Fc difference map, which was derived from Bayesian statistics. This map helps manual and automatic model building in real space, as is common practice in crystallography. The Fo − Fc map helps visualisation of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in electron density maps produced by X-ray crystallography, and some hydrogen atoms are even visible at ∼ 1.8 Å resolution. Servalcat also facilitates atomic model refinement under symmetry constraints. If a point group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with appropriate symmetry constraints.