Extended Data Fig. 3: Cryo-EM data processing workflow (Part 2).
From: Structure of an endogenous mycobacterial MCE lipid transporter
a, Processing pipeline for local refinements performed in cryoSPARC52 and composite map generation. Locally refined maps and raw map for consensus set of particles are shown. Locally refined maps for the consensus set of particles were contoured with the following levels: Map0a (0.281), Map0b (0.257), Map0c (0.259), Map0d (0.199), Map0e (0.17) in ChimeraX53. Map labels are indicated above the map and particle count and average resolution as reported by cryoSPARC are shown below. Composite density maps were generated in PHENIX64. b, Composite Map0 coloured by local resolution that was estimated in cryoSPARC. (left) Whole structure view. Map0 contoured to 12.7. (right) Cross-sectional view. (bottom) key for local resolution colouring, ranging from 2.30 Å (blue) to 4.10 Å (red). c, Gold-standard FSC curve calculated in cryoSPARC for composite, locally refined, and raw maps for consensus set of particles. The dotted line represents the 0.143 FSC cutoff. d, Directional 3DFSC63 calculated for Map0 (composite). e, Locally refined and raw maps for Class 1. Locally refined maps for Class 1 were contoured with the following levels: Map1a (0.172), Map1b (0.201), Map1c (0.185), Map1d (0.167), Map1e (0.15). Map labels are indicated above the map and particle count and average resolution as reported by cryoSPARC are shown below. f, Composite density map for Class 1 (Map1) coloured by local resolution that was estimated in cryoSPARC. (left) Whole structure view. Map1 contoured to 10.1. (right) Cross-sectional view. (bottom) key for local resolution colouring, ranging from 2.30 Å (blue) to 4.10 Å (red). g, Gold-standard FSC curve calculated in cryoSPARC for composite, locally refined, and raw maps for Class 1. The dotted line represents the 0.143 FSC cutoff. h, Directional 3DFSC calculated for Map1 (composite). i, Locally refined and raw maps for Class 2. Locally refined maps for Class 2 were contoured with the following levels: Map2a (0.177), Map2b (0.148), Map2c (0.163), Map2d (0.126), Map2e (0.15). Map label is indicated above the map and particle count and resolution are shown below. j, Composite density map for Class 2 (Map2) coloured by local resolution that was estimated in cryoSPARC. (left) Whole structure view. Map2 contoured to 10.2. (right) Cross-sectional view. (bottom) key for local resolution colouring, ranging from 2.30 Å (blue) to 4.10 Å (red). k, Gold-standard FSC curve calculated in cryoSPARC for composite, locally refined, and raw maps for Class 2. The dotted line represents the 0.143 FSC cutoff. l, Directional 3DFSC calculated for Map2 (composite).
