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Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8F1M experimental model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.468 f_angle_d 0.633 f_chiral_restr 0.039 f_bond_d 0.007 f_plane_restr 0.004
Sample Human nucleosome core particle in complex with RNF168-UbcH5c
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 58264 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 (4GB0, 5EGG) 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) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3500 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 22500 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 2.14 MODEL FITTING PHENIX 1.18.2-3874 INITIAL EULER ASSIGNMENT cryoSPARC 2.14 FINAL EULER ASSIGNMENT cryoSPARC 2.14 CLASSIFICATION cryoSPARC 2.14 RECONSTRUCTION cryoSPARC 2.14 MODEL REFINEMENT PHENIX 1.18.2-3874
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 7889111