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Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LZ0
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 30.0983 f_angle_d 0.6373 f_chiral_restr 0.0423 f_plane_restr 0.0057 f_bond_d 0.0051
Sample Pioneer factor Cbf1 in complex with the nucleosome Sample Components Histone H3.2, Histone H4 Histone H2A.1, Histone H2B.1 Centromere-binding protein 1 DNA
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 73243 Reported Resolution (Å) 3.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (3LZ0) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 18000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 3.2.0 MODEL FITTING PHENIX 1.19.2 INITIAL EULER ASSIGNMENT cryoSPARC 3.2.0 FINAL EULER ASSIGNMENT cryoSPARC 3.2.0 CLASSIFICATION RELION 3.1.2 RECONSTRUCTION cryoSPARC 3.2.0 MODEL REFINEMENT PHENIX 1.19.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION