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Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JBX
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 29.313 f_angle_d 0.749 f_chiral_restr 0.045 f_plane_restr 0.007 f_bond_d 0.004
Sample Human canonical histone and 601 DNA Sample Components Human canonical histone with mutantion C96S/C110S/K115C 601 DNA with an alkynyl-dU modification at position 74 and a Cy5 fluorophore Histone H3.1 Histone H3.1 Histone H4 Histone H2A type 1-B/E Histone H2B type 1-J
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 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 199160 Reported Resolution (Å) 3.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (8JBX) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification 64000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.0.1 MODEL REFINEMENT PHENIX RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 1081772 NONE