Experiment: 6NMI

Cryo-EM structure of the human TFIIH core complex

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OF4
experimental model	PDB	4ERN
experimental model	PDB	5OQJ
experimental model	PDB	1G25
experimental model	PDB	5O85
experimental model	PDB	2DII
experimental model	PDB	2JNJ

Sample
Transcription factor IIH (TFIIH)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	A thin film of continuous carbon was floated onto Protochips C-flat CF-4/2 holey carbon grids and glow discharged or plasma cleaned before application ...	A thin film of continuous carbon was floated onto Protochips C-flat CF-4/2 holey carbon grids and glow discharged or plasma cleaned before application of 4 uL of sample solution.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	138659
Reported Resolution (Å)	3.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (5OF4, 4ERN, 5OQJ, 1G25, 5O85, 2DII, 2JNJ)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Reference structures and homology models were docked and subsequently completely rebuilt according to the density. Parts of the structure were traced ...	Reference structures and homology models were docked and subsequently completely rebuilt according to the density. Parts of the structure were traced de novo.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification	43478
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Residual beam tilt corrected in RELION 3.

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	Gctf
CTF CORRECTION	RELION	3
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot
MODEL FITTING	O
INITIAL EULER ASSIGNMENT	RELION	3
FINAL EULER ASSIGNMENT	RELION	3
CLASSIFICATION	RELION	3
RECONSTRUCTION	RELION	3
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTF correction during 3D reconstruction in RELION 3.