Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structure of the central Staphylococcus aureus AAA+ protease MecA/ClpC/ClpP
Parameter | WT ClpC/ClpP body ClpC w/o NTD and MD (C1) EMDB: 51367 PDB: 9GI1 | WT MecA crown with ClpC NTD and MD (C6) EMDB: 51498 PDB: 9GOQ | WT clpP (D7) EMDB: 53538 PDB: 9R2S | WT MecA/ClpC/ClpP Composite map EMDB: 53879 PDB: 9RAI |
|---|---|---|---|---|
Microscope | Titan Krios G3i (TFS) | Titan Krios G3i (TFS) | Titan Krios G3i (TFS) | Titan Krios G3i (TFS) |
Detector and energy filter | Gatan K3 + Bioquantum(Ametek) | Gatan K3 + Bioquantum(Ametek) | Gatan K3 + Bioquantum(Ametek) | Gatan K3 + Bioquantum(Ametek) |
Nominal magnification (nominal/calibrated at detector) | 105k | 105k | 105k | 105k |
Voltage (kV) | 300 | 300 | 300 | 300 |
Defocus range (µm) | −0.6 to −2.2 | −0.6 to −2.2 | −0.6 to −2.2 | −0.6 to −2.2 |
Total electron exposure (or fluence, e-/Å2) | 40 | 40 | 40 | 40 |
Exposure rate (or flux, e-/pixel/s) | 15 | 15 | 15 | 15 |
Number of frames collected | 40 | 40 | 40 | 40 |
Pixel size (Å) | 0.828 (binned final 1.059) | 0.828 (binned final 1.059) | 0.828 (binned final 1.059) | 0.994 |
Energy filter slit width (eV) | 20 | 20 | 20 | 20 |
Automation software | EPU v3.7 | EPU v3.7 | EPU v3.7 | EPU v3.7 |
# Micrographs used | 12,990 | 12,990 | 12,990 | 12,990 |
Total # of extracted particles | 2,851,121 | 2,851,121 | 2,851,121 | 2,851,121 |
Total # of refined particles (particles after removing junk) | 82,854 | 82,854 | 82,854 | 82,854 |
# of particles in final map | 48,011 | 82,854 | 82,854 | 82,854 |
Resolution of unmasked and masked reconstructions at 0.143 FSC | 4.1/2.9 | 4.0/3.4 | 2.8/2.4 | N/A |
Local resolution range (Å) | 2–6 | 2.3–5.8 | 2.3–3.4 | N/A |
Map sharpening B factor (Å2)/(B factor Range) | −3 | −127 | −66 | N/A |
Model composition | ||||
Non-hydrogen atoms | 47,097 | 13,878 | 19,981 | 60,975 |
Protein residues | 6024 | 1704 | 2591 | 7728 |
Ligands | MG:7, AGS:6;ADP:4 | 0 | 0 | MG:7, AGS:6;ADP:4 |
B factors (Å2) (min/max/mean) | ||||
Protein | 11.7/299.27/127.75 | 103.72/307.67/174.42 | 17.59/187.99/35.69 | 16.58/420.03/83.70 |
Ligand | 79.98/179.82/108.55 | 37.85/119.65/74.77 | ||
Map sharpening EMReady (any) | Yes | Yes | Yes | Yes |
Atomic modeling refinement package(s) | Phenix 1.21 | Phenix 1.21 | Phenix 1.21 | Phenix 1.21 |
Coot 0.95 | Coot 0.95 | Coot 0.95 | Coot 0.95 | |
Isolde | Isolde | Isolde | Isolde | |
CCvolume/CCmask | 0.80 | 0.87 | 0.89 | 0.90 |
0/47,361 (0%) | 0/14,106 | 0/20,236 | 0/61,791 | |
Bad bond lengths and bad bond angles | 1/63,882 (0%) | 0/19,056 | 1/27,315 | 17/83,443 |
Molprobity score | 1.41 | 1.23 | 1.24 | 1.89 |
Clashscore | 3.52 | 1.85 | 2.22 | 10.67 |
Ramachandran plot Z-score | −1.07 | −1.01 | −1 | 1.04 |
Ramachandran Plot (%) | Outliers: 0.34% | Outliers: 0.18% | Outliers: 0.39% | Outliers: 0.04% |
Allowed: 2.94% | Allowed: 3.99% | Allowed: 2.51% | Favored: 96.94% | |
Favored: 96.73% | Favored: 95.83% | Favored: 97.09% | ||
Ramachandran rotamers (%) | Outliers: 1.20% | Outliers: 0.80% | Outliers: 1.26% | Outliers: 1.64% |
Allowed: 5.51% | Allowed: 3.28% | Allowed: 4.93% | Favored: 76.22% | |
Favored: 93.29% | Favored: 95.92% | Favored: 93.82% | ||
CaBLAM outliers (%) | 1.5% | 1.1%o | 1.8% | 1.6% |
EMRinger score | 2.86 (unsharpen)/3.19 (EMReady) | 3.07 (symmetrized) | 4.66 (symmetrized) | N/A |
