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Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LZ0 experimental model PDB 6FTX experimental model PDB 7TN2
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 26.911 f_angle_d 0.701 f_chiral_restr 0.039 f_plane_restr 0.01 f_bond_d 0.004
Sample Nucleosome-Chd1 complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Vitrified carried out in climate chamber with 100% humidity
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 105940 Reported Resolution (Å) 3.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (3LZ0, 6FTX, 7TN2) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target cross-correlation Overall B Value 180 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 46
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1800 Maximum Defocus (nm) 3200 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 81000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.17 IMAGE ACQUISITION EPU 2.8.1 CTF CORRECTION cryoSPARC 4.5.3 MODEL FITTING PHENIX 1.21_5207 MODEL REFINEMENT PHENIX 1.21_5207 INITIAL EULER ASSIGNMENT cryoSPARC 4.5.3 FINAL EULER ASSIGNMENT cryoSPARC 4.5.3 CLASSIFICATION cryoSPARC 4.5.3 RECONSTRUCTION cryoSPARC 4.5.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 2700000