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Fab of O13-1 human IgG1 antibody bound to IgV domain of human TIM-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FQQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 MIB buffer (Sodium malonate dibasic monohydrate, Imidazole, Boric acid), pH 6.0 and 25% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.98 58.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 218.338 α = 90 b = 69.785 β = 99.897 c = 93.632 γ = 90
Symmetry Space Group C 1 2 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 2017-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.97 SSRL BL14-1
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 2.2 38.9 98.3 0.065 0.93 9.1 3.5 69615
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 2.2 2.5 0.66
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 37.003 60928 1218 98.228 0.245 0.2443 0.2711 0.2337 60.959
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] -0.673 -4.112 0.539 1.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.095 r_dihedral_angle_6_deg 14.052 r_lrange_it 8.443 r_lrange_other 8.443 r_dihedral_angle_1_deg 7.25 r_dihedral_angle_2_deg 5.876 r_mcangle_it 5.829 r_mcangle_other 5.828 r_scangle_it 5.119 r_scangle_other 5.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.095 r_dihedral_angle_6_deg 14.052 r_lrange_it 8.443 r_lrange_other 8.443 r_dihedral_angle_1_deg 7.25 r_dihedral_angle_2_deg 5.876 r_mcangle_it 5.829 r_mcangle_other 5.828 r_scangle_it 5.119 r_scangle_other 5.119 r_mcbond_it 3.573 r_mcbond_other 3.573 r_scbond_it 3.049 r_scbond_other 3.049 r_angle_refined_deg 0.964 r_symmetry_xyhbond_nbd_refined 0.374 r_angle_other_deg 0.335 r_xyhbond_nbd_refined 0.309 r_nbd_refined 0.206 r_symmetry_nbd_other 0.192 r_symmetry_nbd_refined 0.181 r_nbtor_refined 0.176 r_nbd_other 0.148 r_ncsr_local_group_3 0.117 r_ncsr_local_group_2 0.096 r_ncsr_local_group_1 0.093 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.042 r_symmetry_xyhbond_nbd_other 0.014 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8259 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing