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EM structure of the DNA wrapping in bacterial open transcription initiation complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YLN
Sample E. coli RNAP-DNA wrapped open complex
Specimen Preparation Sample Aggregation State PARTICLE Staining Type NEGATIVE Staining Material Uranyl Acetate Staining Details Negatively stained EM specimens were prepared using a 2% uranyl acetate solution.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 16015 Reported Resolution (Å) 17 Resolution Method FSC 1/2 BIT CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4YLN) Refinement Space Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Initial fiting was done using manual fitting in Chimera. Yasara software was used for energy minimizaton of the DNA and RNAP coordinates model.
Data Acquisition Detector Type TVIPS TEMCAM-F416 (4k x 4k) Electron Dose (electrons/Å**2) 20
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL 2100 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source LAB6 Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version CTF CORRECTION IMAGIC MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT IMAGIC FINAL EULER ASSIGNMENT IMAGIC CLASSIFICATION IMAGIC RECONSTRUCTION IMAGIC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 60393