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Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from 2.3A and 2.7A Cryo-EM maps
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LZ0 experimental model PDB 3MWY
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 24.302 f_angle_d 0.697 f_chiral_restr 0.066 f_bond_d 0.008 f_plane_restr 0.005
Sample Chd1 ATP-dependent chromatin remodeler bound to a nucleosome
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 450533 Reported Resolution (Å) 2.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (3LZ0, 3MWY) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details phenix.real_space_refine
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 49.9
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2200 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 81000 Calibrated Magnification 46296 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.2 IMAGE ACQUISITION Latitude CTF CORRECTION cryoSPARC 3.2 MODEL FITTING UCSF Chimera MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC 3.2 FINAL EULER ASSIGNMENT cryoSPARC 3.2 CLASSIFICATION cryoSPARC 3.2 RECONSTRUCTION cryoSPARC 3.2 MODEL REFINEMENT PHENIX 1.19.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF amplitude correction was performed following 3D reconstruction 10900948