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F9S, novel TIM-3 targeting antibody, bound to IgV domain of TIM-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Crystals for the TIM-3-F9S Fab complex were obtained in a condition made up of a combination of 0.1M BICINE, pH 9.0 and 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.68 54.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.805 α = 90 b = 57.005 β = 106 c = 80.453 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 100 PIXEL DECTRIS PILATUS 6M Si (111) double crystal 2017-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.987 SSRL BL14-1
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 2.4 35 99.8 0.97 11.2 3.9 23828
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 2.4 2.8 99.9 0.88 3.3
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 THROUGHOUT 2.5 35 22188 1117 99.905 0.194 0.1909 0.1964 0.2412 0.2487 31.428
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] 4.523 -0.607 -2.429 -1.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.972 r_dihedral_angle_2_deg 16.287 r_dihedral_angle_6_deg 16.138 r_dihedral_angle_1_deg 10.58 r_lrange_other 9.241 r_lrange_it 9.233 r_scangle_it 7.316 r_scangle_other 7.315 r_mcangle_it 5.495 r_mcangle_other 5.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.972 r_dihedral_angle_2_deg 16.287 r_dihedral_angle_6_deg 16.138 r_dihedral_angle_1_deg 10.58 r_lrange_other 9.241 r_lrange_it 9.233 r_scangle_it 7.316 r_scangle_other 7.315 r_mcangle_it 5.495 r_mcangle_other 5.494 r_scbond_it 5.124 r_scbond_other 5.123 r_mcbond_it 3.801 r_mcbond_other 3.794 r_angle_refined_deg 0.375 r_xyhbond_nbd_refined 0.255 r_symmetry_nbd_other 0.243 r_nbd_other 0.241 r_nbd_refined 0.227 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.173 r_angle_other_deg 0.139 r_symmetry_nbd_refined 0.128 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.02 r_symmetry_xyhbond_nbd_other 0.005 r_bond_refined_d 0.001 r_gen_planes_refined 0.001 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4145 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing