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Crystal structure of the therapeutic anti-netrin-1 antibody NP137
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BVJ constant domain search models based on PDB ID 5BVJ, while the variable domains were built using RosettaAntibody, which assembles light and heavy chain variable regions by identifying homologous templates and refining the model accordingly
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% w/v Polyethylene glycol 4000, 10% w/v Glycerol, 200 mM Magnesium sulfate
Crystal Properties Matthews coefficient Solvent content 3.43 64.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.434 α = 90 b = 73.441 β = 90 c = 124.005 γ = 90
Symmetry Space Group P 21 21 21
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 1.033200 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 2.9 47.62 100 0.994 9.6 8.7 15255 92.31
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 2.9 3.08 0.547
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5BVJ 2.9 47.62 1.36 15208 1524 99.93 0.223 0.219 0.2163 0.259 0.2572 77.96
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.2277 f_angle_d 0.5728 f_chiral_restr 0.0416 f_plane_restr 0.0042 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3132 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing