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The cryo-EM structure of the mutant MHKKKQ DNMT1-umNCP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JZV experimental model PDB 7XI9 experimental model PDB 3PT6
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 26.798 f_angle_d 0.744 f_chiral_restr 0.039 f_plane_restr 0.006 f_bond_d 0.004
Sample mutant MHKKKQ DNMT1-umNCP complex
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 287638 Reported Resolution (Å) 3.93 Resolution Method FSC 0.5 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7JZV, 7XI9, 3pt6) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 65.5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC MODEL FITTING UCSF Chimera MODEL FITTING Coot MODEL FITTING UCSF ChimeraX MODEL REFINEMENT PHENIX CLASSIFICATION cryoSPARC RECONSTRUCTION PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 7940000