Cryo-EM single-particle structure refinement and map calculation using Servalcat

Yamashita, K.; Palmer, C.M.; Burnley, T.; Murshudov, G.N.

doi:10.1107/S2059798321009475

Acta Crystallographica Section D
Acta Crystallographica
Section D STRUCTURAL BIOLOGY

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Figure 4
Detection of H atoms, measured as the number of observed hydrogen density peaks divided by the number of H atoms in the model. (a) Different apoferritin cases by cryo-EM SPA (see Table 1

). (b) Different (apo)ferritin cases by X-ray crystallography using PDB entries 2v2p, 2v2s, 6gxj, 5erj, 5mij, 2cih, 2w0o, 7bd7, 3f37, 2v2n, 1h96, 2chi, 2zg8, 2v2m, 2z5p, 3h7g, 3f34, 2zg7, 3f32, 3f33, 3f36, 2gyd, 3o7s, 1xz1, 1xz3, 2cn7, 2zg9, 3f38, 2cei, 2iu2, 3fi6, 6env, 3f39, 5ix6, 2v2o, 2v2l, 2v2r, 3o7r, 3rav, 3u90, 3f35, 1aew, 5mik, 2g4h, 2v2i, 3rd0, 5erk, 6ra8, 1gwg, 2clu and 2z5q. (c, d) Apoferritin cases calculated at different resolutions from the same map and model, PDB entry 7a4m/EMDB entry EMD-11638, determined at 1.22 Å resolution. (c) shows detection of H atoms in F_o − F_c maps and (d) in calculated F_c maps. This figure was prepared using ggplot2 (Wickham, 2016