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Cryo-EM structure of CDK2-cyclin A bound to a SCAPER peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.573 f_angle_d 0.424 f_chiral_restr 0.037 f_plane_restr 0.004 f_bond_d 0.002
Sample CDK2-cyclin A bound to a SCAPER peptide
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 91179 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details 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
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) 600 Maximum Defocus (nm) 1800 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 246696 Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v4.4.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC v4.4.1 CTF CORRECTION RELION 5.0 beta MODEL FITTING UCSF ChimeraX MODEL REFINEMENT PHENIX 1.21.1_5286 INITIAL EULER ASSIGNMENT RELION 5.0 beta FINAL EULER ASSIGNMENT RELION 5.0 beta RECONSTRUCTION RELION 5.0 beta
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION