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Cryo-EM structure of CAK-CDK1-cyclin B1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QCV experimental model PDB 5HQ0
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.802 f_angle_d 0.579 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.002
Sample CAK-CDK1-cyclin B1 complex Sample Components CDK-activating kinase (CAK) CDK1-cyclin B1
Specimen Preparation 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 68765 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (9QCV, 5HQ0) 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) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 500 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC CTF CORRECTION RELION 5.0 MODEL FITTING UCSF ChimeraX INITIAL EULER ASSIGNMENT RELION 5.0 FINAL EULER ASSIGNMENT RELION 5.0 CLASSIFICATION RELION 4.0 RECONSTRUCTION RELION 5.0 MODEL REFINEMENT PHENIX 1.21-5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION