5OF4 | pdb_00005of4

The cryo-EM structure of human TFIIH

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	89.082
r_long_range_B_other	89.082
r_scangle_other	64.304
r_mcangle_it	58.665
r_mcangle_other	58.663
r_scbond_it	39.267
r_scbond_other	39.265
r_mcbond_it	36.53
r_mcbond_other	36.529
r_dihedral_angle_2_deg	26.452
r_dihedral_angle_4_deg	14.406
r_dihedral_angle_3_deg	13.555
r_dihedral_angle_1_deg	9.783
r_angle_refined_deg	2.14
r_angle_other_deg	1.229
r_chiral_restr	0.112
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Sample
TFIIH
Sample Components
TFIIH core complex
TFIIH CDK-activating kinase (CAK) subcomplex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	3-4 minute incubation, 2 second blot

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	122900
Reported Resolution (Å)	4.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details	RELION 3D auto-refinement (gold standard).
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial model assembled from high-resolution structures and homology models. Subsequently rebuilt in O and COOT, refined into the cryo-EM map using PHENIX and REFMAC, and fully validated.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN
Minimum Defocus (nm)	2000
Maximum Defocus (nm)	4500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification
Calibrated Magnification	37879
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	Leginon
CTF CORRECTION	CTFFIND	4
MODEL FITTING	UCSF Chimera
MODEL FITTING	O
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	RELION	1.4
FINAL EULER ASSIGNMENT	RELION	1.4
CLASSIFICATION	RELION	1.4
RECONSTRUCTION	RELION	1.4
MODEL REFINEMENT	PHENIX	development versions
MODEL REFINEMENT	REFMAC	5.9

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Correction in RELION based on values determined in CTFFIND4.	1500000	Initial rounds of particle selection using DogPicker within APPION to generate templates for subsequent RELION autopicking.