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Interleukin-31 Receptor D1D2 in complex with Nemolizumab derived scFv
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F3H scFV fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 MorpheusII H6 (40 mM Polyamines, 10% PEG4000, 20% 1,2,6-Hexanetriol, 100 mM BES pH 7)
Crystal Properties Matthews coefficient Solvent content 3.17 61.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.008 α = 90 b = 163.559 β = 90 c = 269.466 γ = 90
Symmetry Space Group C 2 2 21
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 2019-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.147 78.378 99.8 0.112 0.998 10.26 6.73 70477 56.558
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.147 2.28 98.9 1.881 0.302 0.71 5.98
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 2.147 46.745 70223 1995 99.541 0.202 0.2009 0.2005 0.2303 0.2309 66.578
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] 0.284 0.197 -0.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.236 r_dihedral_angle_6_deg 12.49 r_lrange_it 7.801 r_lrange_other 7.801 r_dihedral_angle_1_deg 7.549 r_scangle_it 5.786 r_scangle_other 5.786 r_dihedral_angle_2_deg 5.589 r_mcangle_it 4.067 r_mcangle_other 4.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.236 r_dihedral_angle_6_deg 12.49 r_lrange_it 7.801 r_lrange_other 7.801 r_dihedral_angle_1_deg 7.549 r_scangle_it 5.786 r_scangle_other 5.786 r_dihedral_angle_2_deg 5.589 r_mcangle_it 4.067 r_mcangle_other 4.067 r_scbond_it 3.745 r_scbond_other 3.745 r_mcbond_it 2.713 r_mcbond_other 2.713 r_angle_refined_deg 1.488 r_angle_other_deg 0.517 r_nbd_refined 0.196 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.182 r_nbd_other 0.158 r_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.097 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.067 r_bond_refined_d 0.006 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 6901 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing