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Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F66 experimental model PDB 6FQ5
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 24.338 f_angle_d 0.757 f_chiral_restr 0.042 f_plane_restr 0.022 f_bond_d 0.007
Sample Nucleosome core particle containing variant H2A.Z and canonical core histones Sample Components Histone H3 Histone H4 Histone variant H2A.Z Histone H2B DNA (136-MER) DNA (136-MER)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot for 4.5 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 42826 Reported Resolution (Å) 3.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (1F66, 1F66, 1F66, 1F66, 1F66, 1F66, 1F66, 1F66, 6FQ5, 6FQ5) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target rmsd Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 33
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA 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 FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 92000 Calibrated Magnification 123811 Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1.14 MODEL FITTING RELION 3.1.0 INITIAL EULER ASSIGNMENT RELION 3.1.0 FINAL EULER ASSIGNMENT RELION 3.1.0 CLASSIFICATION RELION 3.1.0 RECONSTRUCTION RELION 3.1.0 MODEL REFINEMENT PHENIX 1.15.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 127778