Abstract
This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.
Highlights
Cryo-EM has emerged as a key method to visualize and model biologically important macromolecules and cellular machines
Map targets representing the state-of-the-art in cryogenic electron microscopy (cryo-EM) single particle reconstruction were selected in the near-atomic resolution regime (1.8–3.1 Å) with a twist: three form a resolution series from the same specimen/imaging experiment
Challenge targets (Fig. 2) consisted of a three-map human heavy-chain apoferritin (APOF) resolution series (a 500-kDa octahedral complex of 24 ɑ-helix-rich subunits), with maps differing only in the number of particles used in reconstruction[8], plus a single map of horse liver alcohol dehydrogenase (ADH)[9]
Summary
Cryo-EM has emerged as a key method to visualize and model biologically important macromolecules and cellular machines. EMDR has convened an EM Validation Task Force[3] analogous to those for X-ray crystallography[4] and NMR5 and has sponsored challenges, workshops and conferences to engage cryo-EM experts, modelers and end-users[2,6]. During this period, cryo-EM has evolved rapidly (Fig. 1). Careful evaluation of submitted models by participating teams leads us to several specific recommendations for validating near-atomic cryo-EM structures, directed toward both individual researchers and the Protein Data Bank (PDB) structure data archive[7]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
