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Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LYA experimental model PDB 4GB0 experimental model PDB 5EGG
Sample Human nucleosome core particle in complex with RNF168 and UbcH5c~Ub
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 85226 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7LYA, 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) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 3000 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.12 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.12 MODEL FITTING PHENIX 1.18.2-3874 MODEL REFINEMENT PHENIX 1.18.2-3874 INITIAL EULER ASSIGNMENT cryoSPARC 4.12 FINAL EULER ASSIGNMENT cryoSPARC 4.12 CLASSIFICATION cryoSPARC 4.12 RECONSTRUCTION cryoSPARC 4.12
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 16063830