3J0K

Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly


ELECTRON MICROSCOPY
Sample
RNA polymerase II VP16-Mediator-pol II-TFIIF assembly
Sample Components
core Mediator
RNA polymerase II
TFIIF
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
Staining TypeNEGATIVE
Staining Materialammonium molybdate
Staining Detailsgrids with adsorbed protein washed 3x with buffer containing 5% trehalose, 20 mM HEPES, 100 mM KCl, and 0.10 mM EDTA, then subjected to cryo-negative ...grids with adsorbed protein washed 3x with buffer containing 5% trehalose, 20 mM HEPES, 100 mM KCl, and 0.10 mM EDTA, then subjected to cryo-negative staining in a saturated solution (1.2M) of ammonium molybdate (pH 7.5)
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles3146
Reported Resolution (Å)36
Resolution MethodFSC 0.5 CUT-OFF
Other DetailsThe particles were selected interactively.
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (1Y1V)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Targetcontour-based Laplacian correlation
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--rigid body DETAILS--the TFIIS chain S was removed before fitting
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)15
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)1000
Maximum Defocus (nm)4500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification29000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGSitus
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
each micrograph