6VAA

Structure of the Fanconi Anemia ID complex bound to ICL DNA


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3S4W 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.436
r_dihedral_angle_4_deg17.499
r_dihedral_angle_3_deg17.443
r_dihedral_angle_1_deg6.951
r_mcangle_it4.734
r_mcangle_other4.733
r_long_range_B_refined3.665
r_long_range_B_other3.665
r_mcbond_it2.885
r_mcbond_other2.885
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.436
r_dihedral_angle_4_deg17.499
r_dihedral_angle_3_deg17.443
r_dihedral_angle_1_deg6.951
r_mcangle_it4.734
r_mcangle_other4.733
r_long_range_B_refined3.665
r_long_range_B_other3.665
r_mcbond_it2.885
r_mcbond_other2.885
r_angle_other_deg1.567
r_angle_refined_deg1.415
r_scangle_other1.223
r_scbond_it0.763
r_scbond_other0.763
r_chiral_restr0.229
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.004
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
FANCI-FANCD2-DNA complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles231943
Reported Resolution (Å)3.4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (3S4W)
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement TargetRfactor
Overall B Value169
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)51
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
CTF CORRECTIONCTFFIND4
MODEL FITTINGO
INITIAL EULER ASSIGNMENTRELION3
MODEL REFINEMENTREFMAC5
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION