Table 1 Cryo-EM data collection and refinement statistics
From: Structural insights into mechanisms of zinc scavenging by the Candida albicans zincophore Pra1
Pra1:Zn2+ complex | Pra1 | |
|---|---|---|
EMD-48872 | EMD-48869 | |
Data collection and processing | PDB-9N4D | PDB-9N47 |
Microscope | Titan Krios | Titan Krios |
Camera | K3/counting | K3/counting |
Magnification | 105,000 | 105,000 |
Energy filter | Gatan | Gatan |
Energy filter slit width (eV) | 20 | 20 |
Collection software | EPU | EPU |
Camera | K3/counting | K3/counting |
Voltage (kV) | 300 | 300 |
Cumulative exposure (e–/Å2) | 63.2 | 63.2 |
Exposure rate (e–/Å2/frame) | 2.1 | 2.1 |
Defocus range (μm) | −1.0 to −2.4 | −1.0 to −2.4 |
Pixel size (Å) | 0.861 | 0.861 |
Symmetry imposed | C1 (none) | C1 (none) |
Number of micrographs | 10,785 | 6886 |
Initial particle images (no.) | 3,486,720 | 1,025,587 |
Final particle images (no.) | 1,102,286 | 607,405 |
0.143 FSC half map masked (Å) | 2.53 | 2.85 |
0.143 FSC half map unmasked(Å) | 3 | 3.3 |
Refinement | ||
Refinement package | Phenix | Phenix |
Initial model used (PDB code) | The AlphaFold model of C. albicans Pra1 as a starting model for manual building | Pra1:zinc model, followed by manual building |
Model resolution range (Å) | 2.25–3.25 | 2.5–3.5 |
Model composition | ||
Non-hydrogen atoms | 10,626 | 10,620 |
Protein residues | 1326 | 1326 |
Ligands | ZN:6 | n/a |
CC map vs. model (%) | 0.90 | 0.90 |
R.m.s. deviations | ||
Bond lengths (Å) | 0.006 | 0.004 |
Bond angles (°) | 1.033 | 0.543 |
Validation | ||
MolProbity score | 1.04 | 1.29 |
Clash score | 0.54 | 1.22 |
Poor rotamers (%) | 1.84 | 2.11 |
Ramachandran plot | ||
Favored (%) | 97.11 | 96.73 |
Allowed (%) | 2.89 | 3.27 |
Outliers (%) | 0 | 0 |
C-beta deviations | 0 | 0 |
EMRinger Score | 3.39 | 3.19 |
CaBLAM outliers (%) | 2.23 | 2.61 |
