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Cryo-EM structure of human full-length RAD52
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KN0
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 2.58 f_angle_d 0.574 f_chiral_restr 0.044 f_bond_d 0.007 f_plane_restr 0.003
Sample Human RAD52 undecameric structure
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 623559 Reported Resolution (Å) 2.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C11
Map-Model Fitting and Refinement Id 1 (1KN0) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation coefficient Overall B Value 130.2 Fitting Procedure Details Initial fitting was done in Chimera followed by refinement with Namdinator and then PHENIX alone
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2200 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details No tilt data and tilted data (30 deg) was collected at the same time and processed together
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3.2 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 3.3.2 MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC RECONSTRUCTION cryoSPARC 3.3.2 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2261059 Template based picking from no tilt and 30 deg tilt data to deal with preferred orientation