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Crystal structure of a novel OX40 antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5 293 0.1m CITRATE, PH5.6, 2% TACSIMATE, 16% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.3 62.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.356 α = 90 b = 162.356 β = 90 c = 232.145 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 PILATUS 12M 2017-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97853 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.3 77.502 99.7 0.168 0.994 9.1 10.6 27927
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.5 1.945 0.67 1.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2EHY 3.303 77.502 22265 1132 80.148 0.198 0.1943 0.2072 0.2681 0.2831 91.616
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] -2.726 -1.363 -2.726 8.842
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 14.564 r_lrange_it 14.563 r_dihedral_angle_6_deg 9.566 r_dihedral_angle_3_deg 9.223 r_mcangle_it 8.38 r_mcangle_other 8.38 r_scangle_it 7.308 r_scangle_other 7.308 r_dihedral_angle_2_deg 5.72 r_mcbond_it 5.523
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 14.564 r_lrange_it 14.563 r_dihedral_angle_6_deg 9.566 r_dihedral_angle_3_deg 9.223 r_mcangle_it 8.38 r_mcangle_other 8.38 r_scangle_it 7.308 r_scangle_other 7.308 r_dihedral_angle_2_deg 5.72 r_mcbond_it 5.523 r_mcbond_other 5.523 r_dihedral_angle_1_deg 4.873 r_scbond_it 4.84 r_scbond_other 4.839 r_rigid_bond_restr 0.683 r_angle_refined_deg 0.593 r_angle_other_deg 0.226 r_nbtor_refined 0.164 r_symmetry_nbd_other 0.162 r_nbd_refined 0.16 r_xyhbond_nbd_refined 0.11 r_symmetry_xyhbond_nbd_refined 0.09 r_symmetry_nbtor_other 0.079 r_nbd_other 0.07 r_symmetry_nbd_refined 0.058 r_chiral_restr 0.027 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8016 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing