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Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RYR experimental model PDB 6JYL
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 24.9095 f_angle_d 0.757 f_chiral_restr 0.0482 f_plane_restr 0.0122 f_bond_d 0.0042
Sample ALC1/CHD1L bound to a PARylated nucleosome
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 5487 Reported Resolution (Å) 4.8 Resolution Method FSC 0.143 CUT-OFF Other Details Non-uniform refinement in cryoSPARC 3.2.0. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6RYR, 6JYL) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Real-space CC Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU 2.6.1 CTF CORRECTION CTFFIND 4.1.9 MODEL FITTING ISOLDE 1.0 INITIAL EULER ASSIGNMENT RELION 3.1.1 FINAL EULER ASSIGNMENT cryoSPARC 3.2.0 CLASSIFICATION cryoSPARC 3.2.0 RECONSTRUCTION cryoSPARC 3.2.0 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 3321590