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RNAP-TopoI complex on duplex scaffold
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ALH experimental model PDB 4RUL
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.218 f_angle_d 0.642 f_chiral_restr 0.055 f_bond_d 0.01 f_plane_restr 0.004
Sample RNAP-TopoI complex on duplex scaffold Sample Components DNA-directed RNA polymerase elongation complex DNA topoisomerase 1
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 113760 Reported Resolution (Å) 2.7 Resolution Method FSC 0.143 CUT-OFF Other Details composite map Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6alh, 4rul) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details Initial rigid body fit was done in UCSF Chimera, followed by flexible fitting in Isolde. The entire model was further refined in Phenix and Coot.
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 56.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.7.6 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC MODEL FITTING UCSF Chimera MODEL FITTING ISOLDE MODEL REFINEMENT PHENIX 1.20.1 MODEL REFINEMENT Coot 0.9.6 INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION