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RNAP-TopoI complex on long-overhang scaffold - orientation 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ALH experimental model PDB 4RUL experimental model PDB 3PX7
Sample RNAP-TopoI complex on long-overhang 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 10189 Reported Resolution (Å) 3.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6alh, 4rul, 3px7) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Initial rigid body fit was done in UCSF chimera, followed by all-atom refinement of RNAP using Phenix and Coot, and flexible fitting of TopoI domains. ... Initial rigid body fit was done in UCSF chimera, followed by all-atom refinement of RNAP using Phenix and Coot, and flexible fitting of TopoI domains.
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 49.9
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2000 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 IMAGE ACQUISITION SerialEM 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