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Structure of SpCas9 with engineered disulfide bonds (R1210C/V1280C and L1119C/P1128C)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7S3H
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.083 f_angle_d 0.442 f_chiral_restr 0.039 f_plane_restr 0.003 f_bond_d 0.002
Sample SpCas9 with engineered disulfide bonds (R1210C/V1280C and L1119C/P1128C)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 610131 Reported Resolution (Å) 3.72 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7S3H) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOCONTINUUM (6k x 4k) Electron Dose (electrons/Å**2) 53
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1800 Maximum Defocus (nm) 2400 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.5.3 IMAGE ACQUISITION SerialEM 4.0.6 CTF CORRECTION cryoSPARC 4.5.3 MODEL FITTING UCSF Chimera 1.17.3 MODEL REFINEMENT PHENIX 1.21.1_5286 INITIAL EULER ASSIGNMENT cryoSPARC 4.5.3 FINAL EULER ASSIGNMENT cryoSPARC 4.5.3 CLASSIFICATION cryoSPARC 4.5.3 RECONSTRUCTION cryoSPARC 4.5.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3618234