8G46

Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.362
r_long_range_B_other16.581
r_long_range_B_refined16.577
r_scangle_other10.079
r_mcangle_it9.391
r_mcangle_other9.391
r_scbond_it6.489
r_scbond_other6.488
r_mcbond_it6.389
r_mcbond_other6.387
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.362
r_long_range_B_other16.581
r_long_range_B_refined16.577
r_scangle_other10.079
r_mcangle_it9.391
r_mcangle_other9.391
r_scbond_it6.489
r_scbond_other6.488
r_mcbond_it6.389
r_mcbond_other6.387
r_dihedral_angle_1_deg5.254
r_dihedral_angle_2_deg2.425
r_angle_refined_deg1.071
r_angle_other_deg0.356
r_chiral_restr0.05
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_bond_other_d
r_dihedral_angle_4_deg
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
Ternary complex of cullin ring E3 ubiquitin ligase substrate receptor arm (DDB1deltaB-DDA1-DCAF16) in compound-induced complex with bromodomain 2 of BRD4
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Detailsdetergent added directly before grid application
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1433050
Reported Resolution (Å)2.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6VIX, 6Q0R)
Refinement Space
Refinement ProtocolOTHER
Refinement Target
Overall B Value74
Fitting Procedure
Detailsrefinement in both real and Fourier space
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50.27
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONTopaz
IMAGE ACQUISITIONSerialEM4.0.5
CTF CORRECTIONcryoSPARC3.3.2
MODEL FITTINGUCSF ChimeraX1.4
INITIAL EULER ASSIGNMENTcryoSPARC3.3.2
FINAL EULER ASSIGNMENTcryoSPARC3.3.2
CLASSIFICATIONcryoSPARC3.3.2
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTISOLDE1.3
MODEL REFINEMENTREFMAC5.8
MODEL REFINEMENTPHENIX1.19
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONin cryoSPARC14452363