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Sortilin-PGRN peptide complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 20.00 %w/ PEG 3350, 0.20 M Sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.72 66.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.945 α = 90 b = 78.618 β = 126.8 c = 111.2 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 2019-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99993 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.87 89.04 98.9 0.034 19.36 3.6 25644
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.87 3.12 98.8 0.43 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT NONE 2.87 44.56 24962 682 99.34 0.25877 0.25803 0.2537 0.2867 0.2862 RANDOM 119.842
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] -7.95 1.48 5.6 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.1 r_dihedral_angle_1_deg 7.094 r_long_range_B_refined 6.642 r_long_range_B_other 6.642 r_mcangle_it 3.02 r_mcangle_other 3.019 r_scangle_other 2.508 r_dihedral_angle_2_deg 2.001 r_mcbond_it 1.657 r_mcbond_other 1.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.1 r_dihedral_angle_1_deg 7.094 r_long_range_B_refined 6.642 r_long_range_B_other 6.642 r_mcangle_it 3.02 r_mcangle_other 3.019 r_scangle_other 2.508 r_dihedral_angle_2_deg 2.001 r_mcbond_it 1.657 r_mcbond_other 1.657 r_scbond_it 1.348 r_scbond_other 1.348 r_angle_refined_deg 1.292 r_angle_other_deg 0.481 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5210 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing