3IYD
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex
ELECTRON MICROSCOPY
Sample |
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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 |
Sample Components |
Catabolite Activator Protein |
lac(ICAP)UP-UV5-bubble |
RNA polymerase holoenzyme (sigma70) |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Staining Type | NEGATIVE |
Staining Material | Uranyl Formate |
Staining Details |
3D Reconstruction | |
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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 ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (1LB2, 1BDF, 2AUK, 1SIG, 3DXJ) | ||||
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 ... |
Data Acquisition | |||||||||
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Detector Type | TVIPS TEMCAM-F415 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 16 |
Imaging Experiment | 1 |
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Date of Experiment | 2008-11-04 |
Temperature (Kelvin) | 293 |
Microscope Model | FEI TECNAI F20 |
Minimum Defocus (nm) | 500 |
Maximum Defocus (nm) | 1500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2 |
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 |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | MODELLER | |
MODEL FITTING | UCSF Chimera | |
MODEL FITTING | Yup.scx | |
RECONSTRUCTION | EMAN | |
RECONSTRUCTION | SPIDER |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
ACE |