Table 2.
Cryo-EM data collection, refinement, and validation statistics (1/2).
| MT-CaKip3-MDC AMP-PNP (EMDB-26074) (PDB 7TQX) |
MT-CaKip3-MDC ADP-AlFx (EMDB-26075) (PDB 7TQY) |
MT-CaKip3-MDC APO (EMDB-26076) (PDB 7TQZ) |
MT-CaKip3-MDN AMP-PNP (EMDB-26077) (PDB 7TR0) |
|
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification (actual) | 60,606 | 58,893 | 60,606 | 60,241 |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 70.4 | 63.3 | 71.1 | 69.6 |
| Defocus range (μm)a | −0.8; −2.1 | −0.8; −1.7 | −0.9; −1.8 | −0.9; −1.7 |
| Pixel size (Å) | 0.825 | 0.849 | 0.825 | 0.830 |
| Symmetry imposedb | Helical | Helical | Helical | Helical |
| Rise (Å) | 5.56 | 5.44 | 5.55 | 5.56 |
| Twist (deg) | 168.09 | 168.07 | 168.09 | 168.09 |
| Particle images identified as 15R symmetry (no.) | 12,120 | 23,783 | 16,061 | 77,728 |
| Particle images in helical reconstruction (no.) | 12,120 | 23,783 | 16,061 | 77,728 |
| Single particles (no.)c | 181,800 | 356,745 | 240,915 | 1,165,920 |
| Single particles used (no.)d | 124,055 | 255,526 | 162,955 | 501,258 |
| Overall resolution (Å) | 2.8 | 2.6 | 2.7 | 2.7 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
| Kinesin resolution (Å) | 3.1 | 2.9 | 3.0 | 2.9 |
| Tubulin resolution (Å) | 2.8 | 2.6 | 2.7 | 2.7 |
| Refinement | ||||
| Model composition | ||||
| Non-hydrogen atoms | 9824 | 9892 | 9791 | 9836 |
| Protein residues | 1229 | 1235 | 1229 | 1229 |
| Ligands | 6 | 7 | 4 | 5 |
| R.m.s. deviations | ||||
| Bond lengths (Å) | 0.0054 | 0.0054 | 0.0061 | 0.0058 |
| Bond angles (°) | 1.14 | 1.17 | 1.19 | 1.17 |
| Validation | ||||
| MolProbity score | 1.48 | 1.36 | 1.48 | 1.36 |
| Clashscore | 4.28 | 3.23 | 5.01 | 4.27 |
| Poor rotamers (%) | 0.47 | 1.12 | 0.94 | 0.66 |
| Ramachandran plot | ||||
| Favored (%) | 96.07 | 96.66 | 96.64 | 97.13 |
| Allowed (%) | 3.93 | 3.34 | 3.36 | 2.87 |
| Disallowed (%) | 0.00 | 0.00 | 0.00 | 0.00 |
| MT-CaKip3-MDNL2-HsKHC AMP-PNP (EMDB-26078) (PDB 7TR1) |
MT-CaKip3-MDNL2-HsKHC APO (EMDB-26079) (PDB 7TR2) |
CT-CaKip3-MDC AMP-PNP (EMDB-26080) (PDB 7TR3) |
|
|---|---|---|---|
| Data collection and processing | |||
| Magnification (actual) | 45,872 | 58,893 | 46,168 |
| Voltage (kV) | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 64.0 | 64.6 | 64.0 |
| Defocus range (μm)a | −0.8; −1.9 | −0.8; −1.7 | −0.9; −3.2 |
| Pixel size (Å) | 1.090 | 0.849 | 1.083 |
| Symmetry imposedb | Helical | Helical | C14 |
| Rise (Å) | 5.54 | 5.55 | |
| Twist (deg) | 168.08 | 168.09 | |
| Particle images identified as 15R/C14 symmetry (no.) | 37,146 | 12,219 | 37,920 |
| Particle images in helical/C14 reconstruction (no.) | 37,146 | 12,219 | 37,920 |
| Single particles (no.)c | 557,190 | 183,285 | 530,936 |
| Single particles used (no.) d | 67,238 | 98,446 | 530,936 |
| Overall resolution (Å) | 3.1 | 3.0 | 3.9 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Kinesin resolution (Å) | 3.4 | 3.4 | 3.9 |
| Tubulin resolution (Å) | 3.0 | 3.0 | 3.9 |
| Refinement | |||
| Model composition | |||
| Non-hydrogen atoms | 9708 | 9588 | 10,224 |
| Protein residues | 1216 | 1207 | 1289 |
| Ligands | 6 | 4 | 4 |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.0055 | 0.0055 | 0.0053 |
| Bond angles (°) | 1.14 | 1.15 | 1.13 |
| Validation | |||
| MolProbity score | 1.44 | 1.37 | 1.90 |
| Clashscore | 3.39 | 3.11 | 7.04 |
| Poor rotamers (%) | 0.19 | 1.05 | 0.36 |
| Ramachandran plot | |||
| Favored (%) | 95.61 | 96.33 | 91.26 |
| Allowed (%) | 4.39 | 3.67 | 8.50 |
| Disallowed (%) | 0.00 | 0.00 | 0.23 |
aRange of the per-particle defocus estimates. The range corresponds to 90% of the particles used, 5% of the particle defocuses are below and 5% are above this range.
bSymmetry imposed during the symmetrical refinement done before the local refinements (rise and twists provided for helical symmetry only).
cTotal number of particles after symmetry expansion.
dNumber of asymmetric units, corresponding to a kinesin motor bound to a tubulin dimer, used after 3D classification.