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

Cryo-EM works by freezing biological molecules which can contain thousands of atoms so they can be imaged under an electron microscope. By aligning and combining many two-dimensional images, researchers can compute three-dimensional maps of an entire molecule, and this technique has been used to study everything from battery failure to the way viruses invade cells. However, an issue that has been hard to solve is how to accurately assess the true level of detail or resolution at every point in such maps and in turn determine what atomic features are truly visible or not.

Wah Chiu, a professor at SLAC and Stanford, Grigore Pintilie, a computational scientist in Chiu's 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 the Stanford-SLAC Cryo-EM Facilities. Kaiming Zhang, another research scientist in Chiu's 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 molecular they 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.

Story Source:

Materials provided by DOE/SLAC National Accelerator Laboratory. Original written by Nathan Collins. Note: Content may be edited for style and length.

Journal Reference:

1. Grigore Pintilie, Kaiming Zhang, Zhaoming Su, Shanshan Li, Michael F. Schmid, Wah Chiu. Measurement of atom resolvability in cryo-EM maps with Q-scores. Nature Methods, 2020; DOI: 10.1038/s41592-020-0731-1