Table 1 Cryo-EM data collection and refinement statistics
KBTBD4WT-UM171-neo-substrate complex | KBTBD4R313PRR-neo-substrate complex | |||
|---|---|---|---|---|
Microscope | Titan Krios | Titan Krios | ||
Detector | K3 | K3 | ||
Voltage (kV) | 300 | 300 | ||
Magnification | 105,000 | 105,000 | ||
Collection mode | Counting | Counting | ||
Electron exposure (e/Å2) | 38.0 | 38.6 | ||
Number of frames | 40 | 40 | ||
Pixel size (Å) | 0.832 | 0.832 | ||
Defocus range (μm; steps) | −1.0 to -3.2 (0.2) | −1.0 to −2.8 (0.2) | ||
Number of movies | 12,722 | 13,131 | ||
Initial Number of particles | 13,588,054 | 19,876,414 | ||
Number of particles after 2D classification | 511,570 | 470,242 | ||
Stoichiometry (KBTBD4:HDAC2:CoREST1) | 2:1:0 | 2:1:1 | 2:2:0 | 2:2:0 |
Number of particles used for 3D refinement | 264,324 | 105,484 | 356,933 | 295,217 |
Symmetry | C1 | C1 | C2 | C2 |
Map resolution (Å; FSC threshold = 0.143) | 3.1 | 3.3 | 2.9* | 2.7** |
Resolution range (Å) | 2.7 – 47.7 | 2.9 – 53.2 | 2.5 – 43.8 | 1.8 – 42.7 |
Map sharpening B-factor (Å2) | −123.7 | −85.1 | −122.7 | −107.7 |
Model resolution(Å; FSC threshold = 0.5) | 3.5 | 3.7 | 3.7 | 3.2 |
Q-score | 0.479 | 0.422 | 0.424 | 0.484 |
Non-hydrogen atoms | 9006 | 9912 | 9936 | 11450 |
Protein residues | 1233 | 1381 | 1434 | 1566 |
Ligands | 2 | 2 | 4 | 2 |
R.M.S.D | ||||
Bond lengths (Å) | 0.004 | 0.001 | 0.003 | 0.005 |
Bond angles (°) | 0.749 | 0.398 | 0.633 | 0.803 |
Validation | ||||
Molprobity score | 1.93 | 1.78 | 1.86 | 2.10 |
Clash score | 13.85 | 5.73 | 5.19 | 11.91 |
Rotamer outliers (%) | 0.24 | 2.25 | 1.52 | 3.07 |
Ramachandran plot | ||||
Favoured (%) | 95.91 | 96.76 | 92.98 | 97.22 |
Allowed (%) | 4.09 | 3.24 | 7302 | 2.78 |
Disallowed (%) | 0 | 0 | 0 | 0 |
EMDB Code | 51335 | 51336 | 51338 | 51337 |
PDB Code | 9GGL | 9I2C | 9GGN | 9GGM |
