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Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OUL
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.744 f_angle_d 0.836 f_chiral_restr 0.055 f_bond_d 0.011 f_plane_restr 0.005
Sample E. coli RNAP-DNA elongation complex 2 (RDe2)
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 76916 Reported Resolution (Å) 2.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6OUL) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 50.46
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION SerialEM MODEL FITTING ISOLDE MODEL REFINEMENT PHENIX 1.16 RECONSTRUCTION cryoSPARC 2.14
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 372776