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Cryo-EM structure of CDK11B-cyclin L2-SAP30BP bound to AMP-PNP
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 4.978 f_angle_d 0.464 f_chiral_restr 0.039 f_plane_restr 0.004 f_bond_d 0.003
Sample CDK11B-cyclin L2-SAP30BP-AMP-PNP complex
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 783863 Reported Resolution (Å) 2.3 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 GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 70
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 600 Maximum Defocus (nm) 1600 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) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.4.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.4.1 CTF CORRECTION RELION 5.0-beta MODEL FITTING UCSF ChimeraX INITIAL EULER ASSIGNMENT RELION 5.0-beta FINAL EULER ASSIGNMENT RELION 5.0-beta CLASSIFICATION RELION 5.0-beta RECONSTRUCTION RELION 5.0-beta MODEL REFINEMENT PHENIX 1.21rc1_4985
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION