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Structure of Pex8 in complex with peroxisomal receptor Pex5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation r_lrange_it 198.505 r_lrange_other 198.503 r_scangle_it 160.124 r_scangle_other 160.11 r_mcangle_it 143.63 r_mcangle_other 143.627 r_scbond_it 98.792 r_scbond_other 98.782 r_mcbond_it 89.139 r_mcbond_other 89.137
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 198.505 r_lrange_other 198.503 r_scangle_it 160.124 r_scangle_other 160.11 r_mcangle_it 143.63 r_mcangle_other 143.627 r_scbond_it 98.792 r_scbond_other 98.782 r_mcbond_it 89.139 r_mcbond_other 89.137 r_dihedral_angle_6_deg 16.532 r_dihedral_angle_3_deg 11.661 r_dihedral_angle_2_deg 6.993 r_dihedral_angle_1_deg 4.519 r_angle_refined_deg 1.932 r_angle_other_deg 0.658 r_nbd_refined 0.228 r_nbtor_refined 0.176 r_symmetry_nbd_other 0.172 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_bond_other_d
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 85869 Reported Resolution (Å) 4.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 64.5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 750 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC MODEL FITTING MOLREP 11.9.02 INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT Servalcat 0.4.32 MODEL REFINEMENT UCSF ChimeraX 1.6.1 MODEL REFINEMENT ISOLDE 1.6.0 MODEL REFINEMENT Coot 0.9.8.5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE