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Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with THZ1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ORM
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.821 f_angle_d 0.483 f_chiral_restr 0.038 f_plane_restr 0.004 f_bond_d 0.002
Sample CDK-activating kinase (CAK)
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 956820 Reported Resolution (Å) 2.6 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 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 700 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 215000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v4.4.1 IMAGE ACQUISITION EPU CTF CORRECTION RELION 5.0 CTF CORRECTION cryoSPARC v4.4.1 MODEL FITTING UCSF ChimeraX 1.2.5 INITIAL EULER ASSIGNMENT RELION 5.0 FINAL EULER ASSIGNMENT RELION 5.0 CLASSIFICATION RELION 5.0 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