Wah Chiu, a professor at SLAC and Stanford, Grigore Pintilie, a computational scientist in Chius group, and colleagues devised the new measures, known as Q-scores, to address that issue. To compute Q-scores, scientists start by building and adjusting an atomic model until it best matches the corresponding cryo-EM derived 3D map. Then, they compare the map to an idealized version in which each atom is well-resolved, revealing to what degree the map truly resolves the atoms in the atomic model.

The researchers validated their approach on large molecules, including a protein called apoferritin that they studied in theStanford-SLAC Cryo-EM Facilities.Kaiming Zhang, another research scientist in Chius group, produced 3D maps close to the highest resolution reached to date up to 1.75 angstrom, less than a fifth of a nanometer. Using such maps,they showed how Q-scores varied in predictable ways based on overall resolution and on which parts of a moleculethey were studying. Pintilie and Chiu say they hope Q-scores will help biologists and others using cryo-EM better understand and interpret the 3D maps and resulting atomic models.

The study was performed in collaboration with researchers from Stanfords Department of Bioengineering. Molecular graphics and analysis were performed using the University of California, San Franciscos Chimera software package. The project was funded by the National Institutes of Health.

Citation: Grigore Pintilie et al.,Nature Methods, February 10, 2020 (10.1038/s41592-020-0731-1)

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Atom or noise? New method helps cryo-EM researchers tell the difference - Stanford University News