Table 1. Cryo-EM data collection, refinement and validation statistics of condensin apo states.
#1 Non-engaged overall (EMD-10951, PDB 6YVU)* | #2 Non-engaged arm segment (EMD-10948) | #3 Non-engaged head segment (EMD-10947) | #4 Bridged overall (EMD-10954) | #5 Bridged arm segment (EMD-10953 | #6 Bridged head segment (EMD-10952, PDB 6YVV) | |
---|---|---|---|---|---|---|
Data collection and processing | ||||||
Magnification | 130k | 105k, 130k | 105k, 130k | 130k | 130k | 130k |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 46.5 | 40 ~ 55 | 40 ~ 55 | 46.5 | 46.5 | 46.5 |
Defocus range (μm) | -0.5 ~ -0.9 | -0.5 ~ -0.9, - 1.6 ~ -3.6 |
-0.5 ~ -0.9, - 1.6 ~ -3.6 |
-0.5 ~ -0.9 | -0.5 ~ -0.9 | -0.5 ~ -0.9 |
Pixel size (Å) | 1.065 | 1.05, 1.065, 1.085, 1.15 |
1.05, 1.065, 1.085, 1.15 |
1.065 | 1.065 | 1.065 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 4,052,794 | 2,369,713 | 1,683,081 | 1,683,081 | 1,683,081 | 1,683,081 |
Final particle images (no.) | 100,388 | 636,446 | 576,016 | 37,639 | 24,593 | |
Map resolution (Å) | 8.1 | 5.3 | 4.2 | 9.1 | 7.8 | 7.5 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 8.1 to >10 | 5.3 to >10 | 4.2 to >10 | 9.1 to >10 | 7.8 to >10 | 7.5 to >10 |
Refinement | ||||||
Initial model used | Ab initio and 4RSI | Homology model derived from 6QJ2, 6QJ4, 4UX3, 6Q6E |
Homology model derived from 6QJ2, 6QJ4, 4UX3, 6Q6E |
|||
Model resolution (Å) | 5.5 | 4.2 | 7.5 | |||
FSC threshold | 0.143 | 0.143 | 0.143 | |||
Model resolution range (Å) | n/a | 4.2 ~ 6.5 | n/a | |||
Map sharpening B factor (Å2) | -276 | -200 | -334 | |||
Model composition | ||||||
Non-hydrogen atoms | 14,952 | |||||
Protein residues | 1,893 | |||||
Ligands | ||||||
B factors (Å2) | ||||||
Protein | 166.71 | |||||
Ligand | ||||||
R.m.s. deviations | 0.004 | |||||
Bond lengths (Å) | 0.941 | |||||
Bond angles (°) | ||||||
Validation | ||||||
MolProbity score | 2.46 | |||||
Clashscore | 24.58 | |||||
Poor rotamers (%) | 0.89 | |||||
Ramachandran plot | ||||||
Favored (%) | 88.77 | |||||
Allowed (%) | 10.69 | |||||
Disallowed (%) | 0.55 |
Pseudo-atomic sub-models of the entire complex were built and refined against the maps #2 (arm) and #3 (head segments), before being assembled into the holo-complex using the overall maps at lower resolution #1