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Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other experimental model PDB 7XD1
Sample DNMT3A1-DNMT3L in complex with a human H2AKc119ub nucleosome wrapped with 195bp of Widom-601 positioning DNA Sample Components H2AKc119ub Nucleosome wrapped with 195 bp Widom601 DNA DNMT3A1-DNMT3L complex Ubiquitin
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 191397 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7XD1) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 50 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 61
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.3.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.3.1 MODEL FITTING ISOLDE 1.6.0 MODEL FITTING UCSF ChimeraX 1.6.1 MODEL REFINEMENT PHENIX 1.20.1-4487 MODEL REFINEMENT Coot 0.9.8.8 INITIAL EULER ASSIGNMENT cryoSPARC 4.3.1 FINAL EULER ASSIGNMENT cryoSPARC 4.3.1 CLASSIFICATION cryoSPARC 4.3.1 RECONSTRUCTION cryoSPARC 4.3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 7826521