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)
Type	Source	Accession Code	Details
experimental model	PDB	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 State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for approximately 2 seconds before plunging into liquid ethane.

3D Reconstruction
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
Id	1 (1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM, 1WCM)	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 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 Type	TVIPS TEMCAM-F415 (4k x 4k)
Electron Dose (electrons/Å**2)	10

Imaging Experiment	1
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
Task	Software Package	Version
MODEL FITTING	OTHER
RECONSTRUCTION	SPARX
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	Each CCD frame

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.