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Cryo-EM structure of the RecBCD in complex with Chi-minus2 substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LD2
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.6916 f_angle_d 0.4182 f_chiral_restr 0.0355 f_plane_restr 0.0053 f_bond_d 0.0016
Sample RecBCD bound to a forked DNA substrate that contain Chi-minus2 Sample Components RecBCD Chi-minus2
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 379790 Reported Resolution (Å) 3.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (5LD2) 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 FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 75.9
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2700 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
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 754150