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Netrin-1 with heparin oligosaccharide ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9D77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2 M Ammonium acetate, 0.1 M Tris pH 8.5, 45% v/v (+/-)-2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 6.07 79.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.774 α = 90 b = 204.774 β = 90 c = 99.233 γ = 120
Symmetry Space Group P 62 2 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 EIGER X 16M Microfocus with variable beam size 1-50 um 2021-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033167 APS 23-ID-B
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 4.083 49.617 93.3 0.118 0.122 0.029 0.993 11.2 21.1 7818 6 163.9
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 4.084 4.404 74 2.571 2.634 0.569 0.205 1.5 21.1
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 THROUGHOUT 4.083 49.234 7805 523 76.602 0.165 0.1606 0.194 0.22 0.2588 RANDOM 270.376
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] -5.122 -2.561 -5.122 16.615
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 48.61 r_scangle_it 41.35 r_mcangle_it 27.059 r_scbond_it 26.702 r_dihedral_angle_1_deg 20.876 r_dihedral_angle_3_deg 18.769 r_mcbond_it 17.241 r_dihedral_angle_6_deg 14.848 r_dihedral_angle_2_deg 5.076 r_angle_refined_deg 1.806
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 48.61 r_scangle_it 41.35 r_mcangle_it 27.059 r_scbond_it 26.702 r_dihedral_angle_1_deg 20.876 r_dihedral_angle_3_deg 18.769 r_mcbond_it 17.241 r_dihedral_angle_6_deg 14.848 r_dihedral_angle_2_deg 5.076 r_angle_refined_deg 1.806 r_nbtor_refined 0.313 r_chiral_restr 0.279 r_symmetry_nbd_refined 0.274 r_symmetry_xyhbond_nbd_refined 0.231 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.166 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3287 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 526
Software Software Software Name Purpose REFMAC refinement JBluIce-EPICS data collection XDS data reduction Aimless data scaling PHASER phasing Coot model building STARANISO data scaling