ELECTRON MICROSCOPY

Sample

E. coli RNA polymerase holoenzyme (sigma70) and E. coli catabolite activator protein (CAP) bound to 98-mer DNA containing the lac promoter and engineered open transcription bubble

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument
Cryogen Name
Sample Vitrification Details
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 14097
Reported Resolution (Å) 19.8
Resolution Method FSC 0.5 CUT-OFF
Other Details EMAN interleaved with SPIDER correspondence analysis ( Details about the particle: 32816 particles were automatically selected by the Appion DoGpicker initially )
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target map-derived potential energy
Overall B Value ?
Fitting Procedure ?
Details REFINEMENT PROTOCOL--rigid body, Yup.scx simulated annealing DETAILS--A complete ternary complex model was generated using multiple PDB entries, with a homology modelling step for RNAP. The model was regularized with PHENIX and the refined against the EM map with Yup.scx using default parameters.
Data Acquisition
Detector Type TVIPS TEMCAM-F415 (4k x 4k)
Electron Dose (electrons/Å2) 16
Imaging Experiment
Date of Experiment 2008-11-04
Temprature (Kelvin)
Microscope Model FEI TECNAI F20
Minimum Defocus (nm) 500
Maximum Defocus (nm) 1500
Minimum Tilt Angle (degrees) 0.0
Maximum Tilt Angle (degrees) 0.0
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Specimen Holder Model SIDE ENTRY, EUCENTRIC
Nominal Magnification 50000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 120
Imaging Details 15 um pixel size on detector
Imaging Experiment
Task Software Package Version
MODEL FITTING MODELLER ?
MODEL FITTING UCSF Chimera ?
MODEL FITTING Yup.scx ?
RECONSTRUCTION EMAN ?
RECONSTRUCTION SPIDER ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
. ACE