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Cryo-EM structure of the human CAK bound to ICEC0942 at 2.5 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XBZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.666 f_angle_d 0.717 f_chiral_restr 0.05 f_bond_d 0.007 f_plane_restr 0.006
Sample CDK-activating kinase (CAK) in complex with ICEC0942
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 205478 Reported Resolution (Å) 2.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6XBZ) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details Real space refinement in PHENIX; ligand coordinates from PHENIX-OPLS3e refinement
Data Acquisition Detector Type GATAN K3 (6k x 4k) GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 69 69
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 500 Maximum Defocus (nm) 1500 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 72886 Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1 IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4.1 CTF CORRECTION RELION 3.1 MODEL FITTING UCSF Chimera MODEL FITTING Coot INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Implemented in RELION 3.1 10904715