Table 1 CryoEM data collection, refinement and validation statistics
From: CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation
DR complex (EMD-20080) (PDB 6OIS) | DDR′ complex (EMD-20081) (PDB 6OIT) | |
|---|---|---|
Data collection and processing | ||
Magnification | 130,000 | 130,000 |
Voltage (kV) | 300 | 300 |
Electron exposure (e–/Å2) | 52.4 | 47.2 |
Defocus range (μm) | −1.5 to −2.5 | −1.5 to −2.5 |
Pixel size (Å) | 1.07 | 1.07 |
Symmetry imposed | C1 | C1 |
Initial particle images (no.) | 1,543,489 | 2,482,628 |
Final particle images (no.) | 314,414 | 620,248 |
Map resolution (Å) | 3.6 | 3.5 |
FSC threshold | 0.143 | 0.143 |
Map resolution range (Å) | 3.0–5.0 | 3.0–5.0 |
Refinement | ||
Initial model used | n/a | n/a |
Model resolution (Å) | 4.6 | 4.0 |
FSC threshold | 0.5 | 0.5 |
Model resolution range (Å) | 4.6 | 4.0 |
Map sharpening B factor (Å2) | −138.9 | −194.1 |
Model composition | ||
Non-hydrogen atoms | 10,732 | 12,085 |
Protein residues | 1365 | 1536 |
Ligands | – | – |
B factors (Å2) | ||
Protein | 75.6 | 30.6 |
Ligand | – | – |
R.m.s. deviations | ||
Bond lengths (Å) | 0.01 | 0.01 |
Bond angles (°) | 1.27 | 1.25 |
Validation | ||
MolProbity score | 1.62 | 1.55 |
Clashscore | 5.99 | 5.33 |
Poor rotamers (%) | 0.59 | 0.53 |
Ramachandran plot | ||
Favored (%) | 95.82 | 96.15 |
Allowed (%) | 4.18 | 3.85 |
Disallowed (%) | 0.00 | 0.00 |
