3J1O
Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RJ1 |
Sample |
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Cryo-EM map of a complex including RNA polymerase II, Mediator Head module, TFIIF, TFIIB, TBP, and promoter DNA |
Sample Components |
mediator head module |
Head module |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | HOMEMADE PLUNGER |
Cryogen Name | ETHANE |
Sample Vitrification Details | Blot for approximately 2 seconds before plunging into liquid ethane. |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 51000 |
Reported Resolution (Å) | 16 |
Resolution Method | FSC 0.5 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (3RJ1, 3RJ1, 3RJ1, 3RJ1, 3RJ1, 3RJ1, 3RJ1) | 2 | |||
Refinement Space | REAL | REAL | |||
Refinement Protocol | RIGID BODY FIT | RIGID BODY FIT | |||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | REFINEMENT PROTOCOL--Rigid body fitting of individual RNA polymerase II structural modules DETAILS--Fitted individual structural modules previously ... | REFINEMENT PROTOCOL--Rigid body fitting of individual Mediator Head structural modules DETAILS--Fitted individual structural modules previously ident ... |
Data Acquisition | |||||||||
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Detector Type | TVIPS TEMCAM-F415 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 10 |
Imaging Experiment | 1 |
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Date of Experiment | 2008-07-30 |
Temperature (Kelvin) | 115 |
Microscope Model | FEI TECNAI F20 |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 3800 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | GATAN LIQUID NITROGEN |
Nominal Magnification | 50000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 120 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | OTHER | |
RECONSTRUCTION | SPARX | |
RECONSTRUCTION | SPIDER |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
Each CCD frame |