5OF4 | pdb_00005of4

The cryo-EM structure of human TFIIH


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined89.082
r_long_range_B_other89.082
r_scangle_other64.304
r_mcangle_it58.665
r_mcangle_other58.663
r_scbond_it39.267
r_scbond_other39.265
r_mcbond_it36.53
r_mcbond_other36.529
r_dihedral_angle_2_deg26.452
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined89.082
r_long_range_B_other89.082
r_scangle_other64.304
r_mcangle_it58.665
r_mcangle_other58.663
r_scbond_it39.267
r_scbond_other39.265
r_mcbond_it36.53
r_mcbond_other36.529
r_dihedral_angle_2_deg26.452
r_dihedral_angle_4_deg14.406
r_dihedral_angle_3_deg13.555
r_dihedral_angle_1_deg9.783
r_angle_refined_deg2.14
r_angle_other_deg1.229
r_chiral_restr0.112
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.003
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 StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details3-4 minute incubation, 2 second blot
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles122900
Reported Resolution (Å)4.4
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsRELION 3D auto-refinement (gold standard).
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsInitial model assembled from high-resolution structures and homology models. Subsequently rebuilt in O and COOT, refined into the cryo-EM map using PH ...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 TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN
Minimum Defocus (nm)2000
Maximum Defocus (nm)4500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification
Calibrated Magnification37879
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONLeginon
CTF CORRECTIONCTFFIND4
MODEL FITTINGUCSF Chimera
MODEL FITTINGO
MODEL FITTINGCoot
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
CLASSIFICATIONRELION1.4
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIXdevelopment versions
MODEL REFINEMENTREFMAC5.9
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCorrection in RELION based on values determined in CTFFIND4.1500000Initial rounds of particle selection using DogPicker within APPION to generate templates for subsequent RELION autopicking.