Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis

摘要

Over the last few years, the technical breakthrough of single-particle cryo electron microscopy (cryo-EM) thanks to the recent developments of direct electron detectors and advanced image processing software (for reviews see, for example, Orlova & Saibil, 2011; Stark & Chari, 2016; Orlov et al, 2017; Kim et al, 2018; Ognjenovic et al, 2019), has in many cases allowed the 3 A resolution range to be reached (Fig. 1). In X-ray crystallography, this resolution range is generally considered to be required for deriving atomic models with properly defined geometrical properties, such as the peptide backbone and side-chain geometry of amino acids and nucleotides in macromolecular complexes. The reason why deriving reliable atomic models is so important is that it provides the basis for the detailed analysis of the three-dimensional structures of interest, such as nucleoprotein complexes in the cell nucleus, membrane proteins or viruses and various drug targets. An atomic model containing flaws because of incorrect or insufficient refinement may lead to incorrect conclusions on the detailed interpretation of the structure, with direct implications on the analysis of interactions between residues. For example, the accurate description of hydrogen bonds (which relies both on proper distances and angular orientations of the acceptor and donor, e.g. Klaholz & Moras, 2002; Coulocheri et al., 2007) are directly relevant for the analysis of molecular recognition or catalysis events, specificity of drug interactions, effects of point mutants etc., and the precise depiction of base-pairing and stacking interactions between nucleotide bases is essential for the analysis of RNA and DNA complexes (Leontis & Westhof, 2001).