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Cryo-EM structure of the RecBCD no Chi negative control complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SJF
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.547 f_angle_d 0.542 f_chiral_restr 0.039 f_plane_restr 0.005 f_bond_d 0.002
Sample RecBCD bound to a forked DNA substrate that does not contain Chi Sample Components RecBCD DNA
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 1s blot before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 62812 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 (6SJF) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details Rounds of manual structure editing in coot and real-space refinement with Phenix
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1400 Maximum Defocus (nm) 2600 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 130000 Calibrated Magnification 47710 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Gautomatch IMAGE ACQUISITION EPU CTF CORRECTION Gctf INITIAL EULER ASSIGNMENT RELION 3 FINAL EULER ASSIGNMENT RELION 3 CLASSIFICATION RELION 3 RECONSTRUCTION RELION 3 MODEL REFINEMENT PHENIX 1.12
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 271210