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Cryo-EM structure of SaCas9-sgRNA-DNA ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CZZ experimental model PDB 5Y36
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.5137 f_angle_d 0.7478 f_chiral_restr 0.0462 f_plane_restr 0.005 f_bond_d 0.0049
Sample SaCas9-sgRNA-target DNA ternary complex Sample Components SaCas9 sgRNA-target DNA
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 217173 Reported Resolution (Å) 3.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5CZZ, 5Y36) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 38
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1800 Maximum Defocus (nm) 2600 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 CTF CORRECTION CTFFIND 4.1 MODEL FITTING Rosetta 3.6 FINAL EULER ASSIGNMENT RELION 3.0.8 CLASSIFICATION RELION 3.0.8 RECONSTRUCTION RELION 3.0.8 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 3872337 We used the program PARSED developed in our previous study to pick the complex particles from the micrographs(Yao R, et al. Bioinformatics. 2020,36:1252-1259).