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Complex of human TfR1 with a potent bicyclic peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In-house generated Apo model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M ammonium tartrate dibasic pH 7.0, 12% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 3.5 64.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.955 α = 90 b = 94.955 β = 90 c = 225.997 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 80x20 2021-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.079 87.542 95.7 0.078 0.08 0.016 1 23.1 24.8 48208
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.079 2.264 75.8 1.256 1.308 0.363 0.769 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.079 87.542 48208 2438 76.422 0.2 0.1983 0.2076 0.2351 0.235 Random selection 52.518
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.079 -0.079 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.938 r_dihedral_angle_6_deg 14.52 r_lrange_it 8.931 r_lrange_other 8.931 r_scangle_it 7.537 r_scangle_other 7.536 r_dihedral_angle_1_deg 7.322 r_dihedral_angle_2_deg 6.472 r_mcangle_it 5.83 r_mcangle_other 5.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.938 r_dihedral_angle_6_deg 14.52 r_lrange_it 8.931 r_lrange_other 8.931 r_scangle_it 7.537 r_scangle_other 7.536 r_dihedral_angle_1_deg 7.322 r_dihedral_angle_2_deg 6.472 r_mcangle_it 5.83 r_mcangle_other 5.829 r_scbond_it 5.24 r_scbond_other 5.239 r_mcbond_it 4.26 r_mcbond_other 4.26 r_dihedral_angle_other_3_deg 2.117 r_angle_refined_deg 1.722 r_angle_other_deg 0.596 r_nbd_refined 0.225 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.181 r_xyhbond_nbd_refined 0.172 r_nbd_other 0.167 r_symmetry_nbd_refined 0.154 r_metal_ion_refined 0.14 r_symmetry_nbtor_other 0.095 r_chiral_restr 0.083 r_symmetry_xyhbond_nbd_other 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5098 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing