Table 1. Cryo-electron microscopy reconstruction information and model refinement statistics and model geometry.
Data collection, processing, and model refinement information for the kinesin-binding protein (KBP), KBP–KIF15_MD6S, and KIF15_MD6S–MT datasets.
| KBP (EMDB: EMD-11338, PDB: 6ZPG) |
KBP–KIF15_MD6S (EMDB: EMD-11339, PDB: 6ZPH) | KIF15_MD6S–MT (EMDB: EMD-11340, PDB: 6ZPI) |
|
|---|---|---|---|
| Data collection and processing | |||
| Pixel size (Å)* | 1.055, 1.043, or 1.047 | 1.047 | 1.39 |
| Number of micrographs (collected, final)* | 9360, 7547 | 6497, 5138 | 214,202 |
| Final particle number | 258,049 (81,628 of which on graphene oxide) | 7513 | 12,674 |
| Map resolution (Å) FSC threshold† |
4.6 Independent half-map FSC 0.143 |
6.9 Independent half-map FSC 0.143 |
4.5 Independent half-map FSC 0.143 |
| Refinement | |||
| Refinement resolution (Å) CC_mask‡ |
4.6
0.64 |
6.9
0.74 |
6
0.60 |
| Map sharpening B-factor (Å2) | −200 | −495 | −134 |
| Model composition Nonhydrogen atoms Protein residues Ligands |
3808 610 0 |
6232 948 1 |
9420 1185 4 |
| R.m.s. deviations§
Bond lengths (Å) Bond angles (°) |
0.01
0.96 |
0.01
1.07 |
0.08
0.17 |
| Validation#
MolProbity score Clashscore Poor rotamers (%) |
1.66
5.25 0.5% |
1.84
7.31 0.9% |
1.95
13.25 0.1% |
| Ramachandran plot#
Favoured (%) Allowed (%) Outliers (%) |
94.38
5.62 0 |
93.13
6.87 0 |
95.38
4.62 0 |
*Inclusive of all data collection sessions.
†The resolution value at the gold-standard Fourier Shell Correlation (FSC) 0.143 criterion between independently refined half-maps.
‡Cross-correlation provided by Phenix real-space refine (Afonine et al., 2018).
§Root-mean-square deviations of bond lengths or angles in the model.
#As defined by the MolProbity validation server (Chen et al., 2010).