Table 1 Cryo-EM data collection, refinement and validation statistics
From: CENP-N promotes the compaction of centromeric chromatin
AN 12-mer (601) (EMDB-26333) | ||||
|---|---|---|---|---|
Data collection and processing | ||||
Magnification | 29,000 | 29,000 | 22,500 | |
Voltage (kV) | 300 | 300 | 300 | |
Electron exposure (e–/Å2) | 70 | 80 | 100 | |
Defocus range (μm) | 0.8–2.0 | 1.0–2.5 | 1.3–2.5 | |
Pixel size (Å) | 0.8211 | 1.02 | 0.655 | |
Symmetry imposed | C1 | C1 | C1 | |
Initial particle images (no.) | 555,254 | 292,321 | 13,356 | |
Final particle images (no.) | 314,239 | 88,530 | 174,936 | 9,305 |
Map resolution (Å) | 2.68 | 3.54 | 5.30 | 12.70 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 2.5–4.5 | 3.5–10 | 5.0–12.0 | 12.5–28.0 |
Refinement | ||||
Initial model used (PDB code) | ||||
Model resolution (Å) | 2.7 | 3.8a | 5.9a | |
FSC threshold | 0.143 | 0.143 | 0.143 | |
Model resolution range (Å) | 2.5–4.5 | 3.5–9.4 | 5.9–11.9 | |
Map sharpening B factor (Å2) | ||||
Model composition | ||||
Non-hydrogen atoms | 13,362 | 26,724 | 262,444 | |
Protein residues | 925 | 1,850 | 1,850 | |
Nucleotide | 290 | 580 | 556 | |
Ligands | 0 | 0 | 0 | |
B factors (Å2) | ||||
Protein | 77.09 | 77.09 | 65.96 | |
Nucleotide | 108.23 | 108.23 | 121.56 | |
Ligand | n/a | n/a | n/a | |
R.m.s. deviations | ||||
Bond lengths (Å) | 0.011 | 0.011 | 0.006 | |
Bond angles (°) | 0.781 | 0.913 | 0.972 | |
Validation | ||||
MolProbity score | 1.38 | 1.4 | 1.58 | |
Clashscore | 4.10 | 4.41 | 4.65 | |
Poor rotamers (%) | 0.00 | 0.00 | 0.00 | |
Ramachandran plot | ||||
Favored (%) | 96.91 | 96.91 | 95.08 | |
Allowed (%) | 3.09 | 3.09 | 4.92 | |
Disallowed (%) | 0.00 | 0.00 | 0.00 | |
