Table 2 Cryo-EM data collection, processing, model building and validation statistics
(Fe-NIAUX)2 consensus (EMD-17731) | (Fe-NIAUSX)2 (EMD-17732) (PDB 8PK8) | (Fe-NSIAUSX)2 (EMD-17733) (PDB 8PK9) | (Fe-NIAU)2 (EMD-17734) (PDB 8PKA) | |
|---|---|---|---|---|
Data collection and processing | ||||
Magnification | ×105,000 (nominal) | ×105,000 (nominal) | ×105,000 (nominal) | ×105,000 (nominal) |
Voltage (kV) | 300 | 300 | 300 | 300 |
Electron exposure (e−/Å2) | 62 | 62 | 62 | 62 |
Defocus range (μm) | −0.8 to −2.5 | −0.8 to −2.5 | −0.8 to −2.5 | −0.8 to −2.5 |
Pixel size (Å) | 0.837 | 0.837 | 0.837 | 0.837 |
Symmetry imposed | C2 | C1 | C1 | C1 |
Initial particle images (no.) | 2,189,680 | 2,189,680 | 2,189,680 | 2,189,680 |
Final particle images (no.) | 696,640 | 507,565 (symmetry expanded) | 393,707 (symmetry expanded) | 269,101 (symmetry expanded) |
Map resolution (Å) FSC threshold | 2.41 0.143 | 2.49 0.143 | 2.58 0.143 | 2.75 0.143 |
Map resolution range (Å) | 2.29–3.29 | 2.37–3.43 | 2.41–3.54 | 2.58–3.68 |
Refinement | ||||
Initial model used (PDB code) | 6NZU | 6NZU | 6NZU | |
Model resolution (Å) FSC threshold | 2.0/2.4 0.143/0.5 | 2.1/2.5 0.143/0.5 | 2.2/2.6 0.143/0.5 | |
Map sharpening B factor (Å2) | −73.3 | a | a | a |
Model composition | ||||
Non-hydrogen atoms | 6461 | 6409 | 5435 | |
Protein residues | 800 | 800 | 680 | |
Ligands | CSS, FE2, PLP, 8Q1 | CSS, FE2, PLP, 8Q1 | FE2, PLP, 8Q1 | |
B factors (Å2) min/max/mean | ||||
Protein Ligand | 6.94/135.86/37.04 18.96/95.18/21.19 | 2.12/87.13/28.96 18.53/75.25/28.50 | 8.66/112.18/35.47 11.28/87.86/25.04 | |
R.m.s. deviations | ||||
Bond lengths (Å) | 0.007 | 0.004 | 0.006 | |
Bond angles (°) | 1.322 | 0.668 | 0.861 | |
Validation | ||||
MolProbity score | 1.68 | 1.62 | 1.75 | |
Clashscore | 6.17 | 6.57 | 6.58 | |
Poor rotamers (%) | 1.61 | 2.20 | 2.75 | |
Ramachandran plot | ||||
Favored (%) | 96.95 | 98.34 | 97.77 | |
Allowed (%) | 2.92 | 1.66 | 2.08 | |
Disallowed (%) | 0.13 | 0.00 | 0.15 | |
