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Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GB0 experimental model PDB 5EGG experimental model Other Crystal structure
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 29.949 f_angle_d 0.634 f_chiral_restr 0.035 f_plane_restr 0.004 f_bond_d 0.003
Sample Human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2)
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 27986 Reported Resolution (Å) 3.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
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 PARTICLE SELECTION cryoSPARC 4.1.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.1.1 MODEL FITTING PHENIX 1.19.2-4158 INITIAL EULER ASSIGNMENT cryoSPARC 4.1.1 FINAL EULER ASSIGNMENT cryoSPARC 4.1.1 CLASSIFICATION RELION 3.0.7 RECONSTRUCTION RELION 3.0.7 MODEL REFINEMENT PHENIX 1.19.2-4158
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 9989935