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Structure of Sortilin ECD in complex with TNFa-targeting SORTAC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PO7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 292.15 22 % PEG6000, 1.1 M NaCl, 8% glycerol, 50 mM HEPES pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.64 66.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.771 α = 90 b = 75.617 β = 127.39 c = 110.197 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M KB mirrors 2025-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.7293 MAX IV BioMAX
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 2.802 79.875 96.9 0.208 0.23 0.096 0.988 7 5.55 25397
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 2.802 2.851 100 2.834 3.119 1.292 0.323 1.3 5.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.802 79.875 25113 1228 95.851 0.214 0.2119 0.2119 0.2532 0.2531 92.821
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] -0.785 1.818 -3.96 0.907
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 14.703 r_lrange_it 14.697 r_dihedral_angle_2_deg 14.225 r_dihedral_angle_3_deg 10.295 r_scangle_it 9.41 r_scangle_other 9.409 r_mcangle_it 7.89 r_mcangle_other 7.889 r_dihedral_angle_6_deg 6.829 r_dihedral_angle_1_deg 6.039
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 14.703 r_lrange_it 14.697 r_dihedral_angle_2_deg 14.225 r_dihedral_angle_3_deg 10.295 r_scangle_it 9.41 r_scangle_other 9.409 r_mcangle_it 7.89 r_mcangle_other 7.889 r_dihedral_angle_6_deg 6.829 r_dihedral_angle_1_deg 6.039 r_scbond_it 5.821 r_scbond_other 5.82 r_mcbond_it 4.877 r_mcbond_other 4.876 r_dihedral_angle_other_2_deg 2.919 r_angle_refined_deg 1.493 r_angle_other_deg 0.521 r_symmetry_xyhbond_nbd_refined 0.326 r_symmetry_nbd_refined 0.268 r_nbd_refined 0.237 r_symmetry_nbd_other 0.213 r_nbd_other 0.191 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.181 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.078 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5180 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 145
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling DIMPLE phasing REFMAC refinement Coot model building