Cryo-EM data collection, refinement, and validation statistics
| . | Nap12•H2A-H2B•Kap114•RanGTP . | Nap12•H2A-H2B•Kap114 . | ||||
|---|---|---|---|---|---|---|
| Consensus map EMD-44151 . | Locally refined map for Nap12•H2A-H2B EMD-44150 . | Composite map PDB: 9B3I EMD-44141 . | Consensus map EMD-44140 . | Locally refined map for Nap12 •H2A-H2B EMD-44137 . | Composite map PDB: 9B3F EMD-44136 . | |
| Data collection and processing | ||||||
| Magnification (X) | 165,000 | 105,000 | ||||
| Voltage (kV) | 300 | 300 | ||||
| Electron exposure (e−/Å2) | 50 | 52 | ||||
| Defocus range (μm) | 0.9–2.2 | 1.5–2.5 | ||||
| Pixel size (Å) | 0.738 | 0.83 | ||||
| Symmetry imposed | C1 | C1 | ||||
| Initial particle images (no.) | 1,381,753 | 4,314,112 | ||||
| Final particle images (no.) | 133,516 | 113,011 | ||||
| Map resolution (Å) | 2.88 | 3.97 | 3.54 | 5.62 | ||
| FSC threshold | 0.143 | |||||
| Refinement | ||||||
| Initial model used (PDB code) | 8F1E, 9B3F | AF-P53067-F1, 8F1E, 9B23 | ||||
| Model composition | ||||||
| Non-hydrogen atoms | 14,951 | 13,451 | ||||
| Protein residues | 1,854 | 1,668 | ||||
| Mean B factors (Å2) | ||||||
| Protein/Ligand | 112.36/40.96 | 317.38 | ||||
| R.m.s. deviations | ||||||
| Bond lengths (Å) | 0.006 | 0.002 | ||||
| Bond angles (°) | 0.781 | 0.505 | ||||
| CCvolume/mask | 0.74/0.73 | 0.70/0.70 | ||||
| Validation | ||||||
| MolProbity score | 1.55 | 1.46 | ||||
| Clashscore | 10.80 | 7.64 | ||||
| Poor rotamers (%) | 0.24 | 0 | ||||
| Ramachandran plot | ||||||
| Favored (%) | 98.20 | 97.82 | ||||
| Allowed (%) | 1.80 | 2.18 | ||||
| Disallowed (%) | 0 | 0 | ||||
| CaBLAM outliers (%) | 0.82 | 1.04 | ||||
| EMRinger score | 2.45 | 0.94 | ||||
| . | Nap12•H2A-H2B•Kap114•RanGTP . | Nap12•H2A-H2B•Kap114 . | ||||
|---|---|---|---|---|---|---|
| Consensus map EMD-44151 . | Locally refined map for Nap12•H2A-H2B EMD-44150 . | Composite map PDB: 9B3I EMD-44141 . | Consensus map EMD-44140 . | Locally refined map for Nap12 •H2A-H2B EMD-44137 . | Composite map PDB: 9B3F EMD-44136 . | |
| Data collection and processing | ||||||
| Magnification (X) | 165,000 | 105,000 | ||||
| Voltage (kV) | 300 | 300 | ||||
| Electron exposure (e−/Å2) | 50 | 52 | ||||
| Defocus range (μm) | 0.9–2.2 | 1.5–2.5 | ||||
| Pixel size (Å) | 0.738 | 0.83 | ||||
| Symmetry imposed | C1 | C1 | ||||
| Initial particle images (no.) | 1,381,753 | 4,314,112 | ||||
| Final particle images (no.) | 133,516 | 113,011 | ||||
| Map resolution (Å) | 2.88 | 3.97 | 3.54 | 5.62 | ||
| FSC threshold | 0.143 | |||||
| Refinement | ||||||
| Initial model used (PDB code) | 8F1E, 9B3F | AF-P53067-F1, 8F1E, 9B23 | ||||
| Model composition | ||||||
| Non-hydrogen atoms | 14,951 | 13,451 | ||||
| Protein residues | 1,854 | 1,668 | ||||
| Mean B factors (Å2) | ||||||
| Protein/Ligand | 112.36/40.96 | 317.38 | ||||
| R.m.s. deviations | ||||||
| Bond lengths (Å) | 0.006 | 0.002 | ||||
| Bond angles (°) | 0.781 | 0.505 | ||||
| CCvolume/mask | 0.74/0.73 | 0.70/0.70 | ||||
| Validation | ||||||
| MolProbity score | 1.55 | 1.46 | ||||
| Clashscore | 10.80 | 7.64 | ||||
| Poor rotamers (%) | 0.24 | 0 | ||||
| Ramachandran plot | ||||||
| Favored (%) | 98.20 | 97.82 | ||||
| Allowed (%) | 1.80 | 2.18 | ||||
| Disallowed (%) | 0 | 0 | ||||
| CaBLAM outliers (%) | 0.82 | 1.04 | ||||
| EMRinger score | 2.45 | 0.94 | ||||