Table 1 CryoEM data collection, processing, model building, and validation statistics
From: A proteolytic AAA+ machine poised to unfold protein substrates
Sample and data deposition information | |||
|---|---|---|---|
Sample name | ClpX∆N•ClpP•branched-DHFR•MTX | ClpX∆N•ClpP•linear-DHFR•MTX | ClpX∆N•ClpP•branched-DHFR |
Nucleotide added | ATP | ATP | ATP |
PDB code | 8V9R | 9C87 | 9C88 |
EMDB ID | 43081 | 45299 | 45300 |
Data collection and image processing | |||
Microscope | Titan Krios G3i | Titan Krios G2 | Titan Krios G2 |
Camera | Gatan K3 (counting mode) | Gatan K3 (counting mode) | Gatan K3 (counting mode) |
Magnification (nominal) | 130,000 X | 130,000 X | 130,000 X |
Accelerating voltage (kV) | 300 | 300 | 300 |
Total electron dose (e-/Å2) | 51.94 | 47.54 | 47.54 |
Defocus range (µm) | -0.5 to -1.8 | -0.5 to -1.75 | -0.5 to -1.75 |
Micrographs collected | 15,920 | 15,864 | 14,574 |
Pixel size (Å) initial/calibrated | 0.679 / 0.654 | 0.65 | 0.65 |
Map reconstruction | |||
Image processing package | cryoSPARC | ||
Total extracted ClpXP particles | 1,005,797 | 355,300 | 434,826 |
Final particle count | 449,424 | 71,203 | 178,399 |
Symmetry imposed | C1 | C1 | C1 |
Resolution (Å) | |||
0.143 GSFSC unmasked | 3.3 | 4.4 | 3.3 |
0.143 GSFSC spherical mask | 3.1 | 4.1 | 3.0 |
0.143 GSFSC tight/local mask | 2.8 | 3.7 | 2.6 |
3DFSC sphericity (out of 1.0) | 0.986 | 0.931 | 0.972 |
Model composition | |||
Number of atoms | 72,633 | 77,422 | 74,036 |
Protein residues | 4,955 | 4,943 | 4,733 |
Ligands | ATP (3); ADP (3) Mg (4); MTX (1) | ATP (3); ADP (3) Mg (4); MTX (1) | ATP (3); ADP (3) Mg (4) |
Model refinement | |||
Refinement package | Phenix and Coot | Phenix and Coot | |
Map-to-model cross correlation | |||
masked | 0.81 | 0.75 | 0.81 |
unmasked | 0.83 | 0.84 | 0.78 |
RMSD bond lengths (Å) [#>4σ] | 0.003 [0] | 0.002 [0] | 0.002 [0] |
RMSD bond angles (°) [#>4σ] | 0.666 [0] | 0.653 [0] | 0.501 [0] |
Model validation | |||
MolProbity score | 0.94 | 1.03 | 0.89 |
Clash score | 1.80 | 2.48 | 1.04 |
C-beta outliers (%) | 0.02 | 0.02 | 0.0 |
Rotamer outliers (%) | 0.0 | 0.0 | 0.003 |
Ramachandran favored (%) | 99.5 | 99.9 | 97.6 |
Q-Score [mean] | |||
Global / expected from resolution | 0.62 / 0.61 | 0.47 / 0.45 | 0.63 / 0.65 |
ClpX | 0.61 | 0.47 | 0.54 |
ClpPcis | 0.71 | 0.56 | 0.66 |
DHFR | 0.60 | 0.22 | 0.72 |
