5OF4
The cryo-EM structure of human TFIIH
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_long_range_B_refined | 89.082 |
r_long_range_B_other | 89.082 |
r_scangle_other | 64.304 |
r_mcangle_it | 58.665 |
r_mcangle_other | 58.663 |
r_scbond_it | 39.267 |
r_scbond_other | 39.265 |
r_mcbond_it | 36.53 |
r_mcbond_other | 36.529 |
r_dihedral_angle_2_deg | 26.452 |
Sample |
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TFIIH |
Sample Components |
TFIIH core complex |
TFIIH CDK-activating kinase (CAK) subcomplex |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 3-4 minute incubation, 2 second blot |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 122900 |
Reported Resolution (Å) | 4.4 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | RELION 3D auto-refinement (gold standard). |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | Initial model assembled from high-resolution structures and homology models. Subsequently rebuilt in O and COOT, refined into the cryo-EM map using PH ... |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN |
Minimum Defocus (nm) | 2000 |
Maximum Defocus (nm) | 4500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Nominal Magnification | |
Calibrated Magnification | 37879 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
IMAGE ACQUISITION | Leginon | |
CTF CORRECTION | CTFFIND | 4 |
MODEL FITTING | UCSF Chimera | |
MODEL FITTING | O | |
MODEL FITTING | Coot | |
INITIAL EULER ASSIGNMENT | RELION | 1.4 |
FINAL EULER ASSIGNMENT | RELION | 1.4 |
CLASSIFICATION | RELION | 1.4 |
RECONSTRUCTION | RELION | 1.4 |
MODEL REFINEMENT | PHENIX | development versions |
MODEL REFINEMENT | REFMAC | 5.9 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | Correction in RELION based on values determined in CTFFIND4. | 1500000 | Initial rounds of particle selection using DogPicker within APPION to generate templates for subsequent RELION autopicking. |