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Crystal structure of netrin-1 in complex with anti-netrin-1 Fab (NP137 Fab)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LRF experimental model PDB 9OHH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 18% PEG8000, 100 mM HEPES pH 7.5, 200 mM Ca Acetate
Crystal Properties Matthews coefficient Solvent content 3.14 60.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.984 α = 90 b = 263.049 β = 92.512 c = 68.765 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS3 6M 2021-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 4.99 49.39 97.08 0.99 5.4 3.3 9577
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.99 5.41 0.48
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 4.99 49.39 9567 966 90.967 0.29 0.2861 0.3026 0.3211 0.3068 RANDOM 48.504
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] -59.209 -2.1 -71.782 130.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.506 r_dihedral_angle_6_deg 13.515 r_dihedral_angle_1_deg 6.419 r_angle_refined_deg 1.04 r_angle_other_deg 0.38 r_metal_ion_refined 0.254 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.186 r_nbd_refined 0.185 r_nbtor_refined 0.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.506 r_dihedral_angle_6_deg 13.515 r_dihedral_angle_1_deg 6.419 r_angle_refined_deg 1.04 r_angle_other_deg 0.38 r_metal_ion_refined 0.254 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.186 r_nbd_refined 0.185 r_nbtor_refined 0.171 r_nbd_other 0.147 r_ncsr_local_group_1 0.102 r_symmetry_xyhbond_nbd_other 0.096 r_symmetry_nbd_refined 0.093 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_3 0.074 r_ncsr_local_group_2 0.071 r_chiral_restr 0.05 r_ext_dist_refined_b 0.03 r_bond_refined_d 0.008 r_symmetry_xyhbond_nbd_refined 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10403 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing