8P79
Cryo-EM structure of CAK with averaged inhibitor density
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 8ORM |
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.913 |
r_dihedral_angle_4_deg | 17.264 |
r_dihedral_angle_3_deg | 14.417 |
r_long_range_B_refined | 7.741 |
r_long_range_B_other | 7.739 |
r_dihedral_angle_1_deg | 5.638 |
r_scangle_other | 4.892 |
r_mcangle_it | 4.395 |
r_mcangle_other | 4.394 |
r_scbond_it | 3 |
Sample |
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CDK-activating kinase |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 2060053 |
Reported Resolution (Å) | 1.7 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (8ORM) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | TFS FALCON 4i (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 70 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | TFS KRIOS |
Minimum Defocus (nm) | 400 |
Maximum Defocus (nm) | 1900 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | |
Calibrated Magnification | 245614 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | v3.3.1 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | RELION | 4.0 beta |
CTF CORRECTION | cryoSPARC | v3.3.1 |
MODEL FITTING | UCSF ChimeraX | 1.2.5 |
MODEL REFINEMENT | REFMAC | 5.8.0267 |
INITIAL EULER ASSIGNMENT | RELION | 4.0 beta |
FINAL EULER ASSIGNMENT | RELION | 4.0 beta |
CLASSIFICATION | RELION | 4.0 beta |
RECONSTRUCTION | RELION | 4.0 beta |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |