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Activated wild-type SgrAI endonuclease DNA-bound dimer with Mg2+ and cleaved primary site DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OBJ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.324 f_angle_d 0.491 f_chiral_restr 0.04 f_bond_d 0.004 f_plane_restr 0.004
Sample Activated wild-type filamentous SgrAI endonuclease with Mg2+ and cleaved primary site DNA
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument HOMEMADE PLUNGER Cryogen Name ETHANE Sample Vitrification Details Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C
3D Reconstruction Reconstruction Method HELICAL Number of Particles 202664 Reported Resolution (Å) 3.05 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C2 Axial Rise 21.3 Angular Rotation -86.2
Map-Model Fitting and Refinement Id 1 (6OBJ) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Correlation coefficient Overall B Value 87.9 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 29.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2000 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 165000 Calibrated Magnification 60240 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC MODEL FITTING Coot MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT RELION 4.2 RECONSTRUCTION cryoSPARC 4.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION