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Crystal structure of bivalent antibody Fab fragment of Anti-human LAG3 (22D2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WKM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.1 M Tris-HCl, pH 7.5, 0.2 M sodium chloride, 10% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 3.17 61.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.287 α = 90 b = 44.39 β = 106.136 c = 89.084 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 2021-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03 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 2.83 85.57 92.9 0.98 13.7 2 13587
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 2.83 2.9 0.68
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 PDB entry 6WKM 2.833 42.75 13587 706 92.903 0.219 0.2164 0.217 0.2767 0.2726 77.32
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] -3.808 -1.694 10.894 -5.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.039 r_dihedral_angle_4_deg 18.474 r_dihedral_angle_3_deg 17.024 r_lrange_it 15.314 r_lrange_other 15.303 r_scangle_it 9.767 r_scangle_other 9.765 r_mcangle_it 9.182 r_mcangle_other 9.18 r_dihedral_angle_1_deg 7.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.039 r_dihedral_angle_4_deg 18.474 r_dihedral_angle_3_deg 17.024 r_lrange_it 15.314 r_lrange_other 15.303 r_scangle_it 9.767 r_scangle_other 9.765 r_mcangle_it 9.182 r_mcangle_other 9.18 r_dihedral_angle_1_deg 7.019 r_scbond_it 6.332 r_scbond_other 6.33 r_mcbond_it 6.035 r_mcbond_other 6.034 r_angle_refined_deg 1.397 r_angle_other_deg 1.279 r_symmetry_xyhbond_nbd_refined 0.275 r_xyhbond_nbd_other 0.27 r_nbd_refined 0.236 r_symmetry_nbd_other 0.204 r_nbd_other 0.191 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.152 r_xyhbond_nbd_refined 0.146 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3145 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing