3IYD
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex
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 |
| Sample Components |
| Catabolite Activator Protein |
| lac(ICAP)UP-UV5-bubble |
| RNA polymerase holoenzyme (sigma70) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Staining Type | NEGATIVE |
| Staining Material | Uranyl Formate |
| Staining 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 ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| 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 | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TVIPS TEMCAM-F415 (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 16 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| 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 | ||
|---|---|---|
| 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 | ||||
