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Activated SgrAI endonuclease DNA-bound dimer with Ca2+ and intact 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 21.974 f_angle_d 0.54 f_chiral_restr 0.04 f_plane_restr 0.004 f_bond_d 0.003
Sample Activated filamentous SgrAI endonuclease with Ca2+ and intact 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 220067 Reported Resolution (Å) 2.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 21.2 Angular Rotation -85.8
Map-Model Fitting and Refinement Id 1 (6OBJ) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Correlation coefficient Overall B Value 107.7 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 55
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 Warp MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION