Table 2 Cryo-EM data collection, refinement and validation statistics for G. haemolysans IgA1P res. 907-2201 and the IgA1P-E1848A mutation in complex with IgA1.
From: A substrate-induced gating mechanism is conserved among Gram-positive IgA1 metalloproteases
IgA1P | IgA1P + IgA1 | |
|---|---|---|
Data Collection and Processing | ||
Microscope | Titan Krios | Titan Krios |
Voltage (kV) | 300 | 300 |
Magnification (nominal) | 105,000 | 29,000 |
Electron Dose (e-/Å2) | 46 | 49 |
Camera | Gatan K3 BioQuantum | Gatan K3 |
Defocus range (um) | −0.7 to −2.0 | −0.8 to −2.3 |
Pixel size (Å) super resolution | 0.415 | 0.401 |
Movies collected | 6,367 | 11,568 |
Symmetry imposed | C1 | C1 |
Final particle images (no.) | 443,908 | 205,808 |
Map resolution (Å) | 3.25 | 3.53 |
Sharpening B-factor (Å2) | 160.2 | 109.4 |
Software used to process data | cryoSPARC | cryoSPARC |
Refinement statistics | ||
Number of protein atoms (non-H) | 10,350 | 16,508 |
R.m.s. deviations | – | – |
Bonds (Å) | 0.007 | 0.008 |
Bond angles (°) | 1.020 | 1.006 |
Validation | – | – |
MolProbity score | 2.09 | 2.92 |
Clash score | 9.63 | 13.35 |
Poor rotamers (%) | 1.02 | 0 |
Ramachandran plot | – | – |
Favored (%) | 91.59 | 94.82 |
Allowed (%) | 8.41 | 5.18 |
Disallowed (%) | 0 | 0 |
C-beta deviations | 0 | 0 |
Model vs Data CC | 0.83 | 0.82 |
FSC model (0.143) | 3.7 | 3.8 |
EMDB access code | EMD-26812 | EMD-26813 |
PDB access code | 7UVK | 7UVL |
