Table 1 Data collection, processing, and model validation table for D1-2, D1-3, and D1-4
From: Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy
D1-2 | D1-3 | D1-4 | ||||
|---|---|---|---|---|---|---|
State | partly open | fully open | partly open | fully open | partly open | fully open |
PDB id | 9G4I | 9G4V | 9G4L | 9G4J | 9G54 | 9G56 |
EMDB id | EMD-51040 | EMD-51068 | EMD-51044 | EMD-51041 | EMD-51077 | EMD-51080 |
Data Collection | ||||||
Magnification | 105,000 | 105,000 | 105,000 | 105,000 | 130,000 | 130,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
Data collection mode | Counting | Counting | Super resolution | Super resolution | Counting | Counting |
Electron exposure (e–/Å2) | 38.07 | 38.07 | 40 | 40 | 40 | 40 |
Defocus range (μm) | 0.8–2.2 | 0.8–2.2 | 0.8–2.2 | 0.8–2.2 | 0.8–1.8 | 0.8–1.8 |
Pixel size (Å) | 0.839 | 0.839 | 0.42 | 0.42 | 0.81 | 0.81 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particle images (No.) | 306,972 | 306,972 | 615, 617 | 615, 617 | 349,634 | 349,634 |
Processing | ||||||
Name of the map | Partly open | Fully open | Partly open | Fully open | Partly open | Fully open |
Final particle images (no.) | 41,652 | 39,075 | 18,005 | 16,493 | 41,981 | 56,717 |
Map resolution (Å) | 4.61 | 4.69 | 4.01 | 3.74 | 6.30 | 7.54 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map local resolution range (Å) (FSC Threshold 0.5) | 4.0-6.7 | 4.1-6.8 | 3.6-9.5 | 3.5-9.2 | 7.0-10.0 | 7.0-10.0 |
Model Refinement | ||||||
Geometry refinement | ERRASER | ERRASER | ERRASER | ERRASER | - | - |
Real space refinement | TEMPy-ReFF | TEMPy-ReFF | TEMPy-ReFF | TEMPy-ReFF | TEMPy-ReFF | TEMPy-ReFF |
Initial model used (PDB id) | 4FAQ | 4FAQ | 4FAQ | 4FAQ | 4FAQ | 4FAQ |
Model resolution (Å) | 4.6 | 4.7 | 4 | 3.7 | 6.5 | 7.5 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Model composition | ||||||
Total atoms | 5845 | 4715 | 5714 | 5157 | 6288 | 4631 |
Hydrogen atoms | 0 | 0 | 0 | 0 | 0 | 0 |
Non-hydrogen atoms | 5845 | 4715 | 5714 | 5157 | 6288 | 4631 |
Nucleotide | 273 | 221 | 267 | 241 | 293 | 217 |
R.M.S. deviations / (num. outliers) | ||||||
Bond lengths (Å) | 0.014(0) | 0.014(0) | 0.014(0) | 0.014(0) | 0.014(0) | 0.014(0) |
Bond angles (°) | 1.72 (29) | 153 (8) | 1.48 (9) | 1.47 (8) | 1.78 (57) | 1.75 (27) |
Validation | ||||||
Validation software | Phenix | Phenix | Phenix | Phenix | Phenix | Phenix |
MolProbity score | 1.77 | 1.65 | 1.65 | 1.65 | 1.69 | 1.71 |
Clashscore | 0.34 | 0.00 | 0.00 | 0.00 | 0.11 | 0.14 |
CCmask | 0.85 | 0.85 | 0.86 | 0.86 | 0.90 | 0.86 |
CCpeak | 0.79 | 0.73 | 0.79 | 0.77 | 0.82 | 0.70 |
CCvolume | 0.84 | 0.84 | 0.86 | 0.86 | 085 | 0.79 |
Average Suitness | 0.508 | 0.553 | 0.666 | 0.669 | 0.490 | 0.441 |
Validation software | TEMPy | TEMPy | TEMPy | TEMPy | TEMPy | TEMPy |
SMOC Score | 0.90 | 0.90 | 0.87 | 0.83 | 0.91 | 0.92 |
