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Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated FANCI and to DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S4W
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.077 r_dihedral_angle_4_deg 18.063 r_dihedral_angle_3_deg 16.262 r_long_range_B_refined 10.629 r_long_range_B_other 10.629 r_dihedral_angle_1_deg 8.457 r_mcangle_it 5.731 r_mcangle_other 5.731 r_scangle_other 5.504 r_mcbond_it 3.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.077 r_dihedral_angle_4_deg 18.063 r_dihedral_angle_3_deg 16.262 r_long_range_B_refined 10.629 r_long_range_B_other 10.629 r_dihedral_angle_1_deg 8.457 r_mcangle_it 5.731 r_mcangle_other 5.731 r_scangle_other 5.504 r_mcbond_it 3.209 r_mcbond_other 3.209 r_scbond_it 3.071 r_scbond_other 3.071 r_angle_refined_deg 1.659 r_angle_other_deg 1.525 r_chiral_restr 0.157 r_bond_other_d 0.013 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 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 Mono-ubiquitinated FANCD2 bound to non-ubiquitinated FANCI and to DNA
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 57993 Reported Resolution (Å) 3.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (3S4W) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target R-factor Overall B Value 195 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 51
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION CTFFIND 4 MODEL FITTING O INITIAL EULER ASSIGNMENT RELION 3 MODEL REFINEMENT REFMAC 5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION