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 3J1N | pdb_00003j1n

Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WCM 
Sample
Cryo-EM map of a complex including RNA polymerase II, Mediator Head module, TFIIF, TFIIB, TBP, and promoter DNA
Sample Components
RNA polymerase II
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsBlot for approximately 2 seconds before plunging into liquid ethane.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles51000
Reported Resolution (Å)16
Resolution MethodFSC 0.5 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM)2
Refinement SpaceREALREAL
Refinement ProtocolRIGID BODY FITRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--Rigid body fitting of individual RNA polymerase II structural modules DETAILS--Fitted individual structural modules previously ...REFINEMENT PROTOCOL--Rigid body fitting of individual RNA polymerase II structural modules DETAILS--Fitted individual structural modules previously identified by X-ray crystallographic studies of RNA polymerase II under different crystallization conditions
REFINEMENT PROTOCOL--Rigid body fitting of individual Mediator Head structural modules DETAILS--Fitted individual structural modules previously ident ...REFINEMENT PROTOCOL--Rigid body fitting of individual Mediator Head structural modules DETAILS--Fitted individual structural modules previously identified by EM and X-ray crystallographic studies of the Head module
Data Acquisition
Detector TypeTVIPS TEMCAM-F415 (4k x 4k)
Electron Dose (electrons/Å**2)10
Imaging Experiment1
Date of Experiment2008-07-30
Temperature (Kelvin)115
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)800
Maximum Defocus (nm)3800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification50000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)120
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGOTHER
RECONSTRUCTIONSPARX
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
Each CCD frame