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Structure of S79 Fab in complex with IgV domain of human PD-L1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FN3 experimental model PDB 5VEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1M Tris pH 8.0, 1.6M Li2SO4
Crystal Properties Matthews coefficient Solvent content 4.21 70.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.852 α = 90 b = 185.852 β = 90 c = 110.237 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 EIGER X 16M 2022-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9763 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.79 48.24 99.7 0.205 0.043 0.995 11.8 24 28276
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.94 98.1 3.089 0.637 0.622 1.3 23.9
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.794 48.24 28249 1385 99.8 0.23 0.2289 0.2508 0.2363 RANDOM 119.06
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] -3.0203 -3.0203 6.0406
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.79 t_omega_torsion 3.26 t_angle_deg 0.96 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_utility_distance t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4124 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 49
Software Software Software Name Purpose BUSTER refinement PHASER phasing Aimless data scaling XDS data reduction MxCuBE data collection