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Figure 6
Confidence maps confirm the localization of nonprotein components. (a) β-Galactosidase (EMD-2984) with 3.5/4.5σ-thresholded cryo-EM maps (left and center, gray) and a 1% FDR-thresholded confidence map (right, blue). Top: the Mg2+ ion is coordinated by Glu461, Glu416, His418 and three H2O molecules. Bottom: density of bound PETG ligand in 3.5/4.5σ-thresholded cryo-EM maps and the 1% FDR confidence map. (b) TRPV1 channel (EMD-5778) with a 5σ-thresholded cryo-EM map (left) and a 1% FDR-thresholded confidence map (right): the selectivity filter formed by the carbonyls of symmetry-related Gly643 residues. The presence of a putative ion is supported by the confidence map. (c) γ-Secretase (EMD-3061) with 4σ- and 5σ-thresholded cryo-EM maps (left) and a 1% FDR-thresholded confidence map (right). The confidence map reveals density for both acyl chains of phosphatidylcholine at a single threshold.

IUCrJ
Volume 6| Part 1| January 2019| Pages 18-33
ISSN: 2052-2525
https://doi.org/10.1107/S2052252518014434