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Structure of human PD-L1 in complex with clinically evaluated inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J89
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.066 α = 90 b = 72.066 β = 90 c = 89.048 γ = 120
Symmetry Space Group P 31 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 2024-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.968 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.1 62.41 94.9 0.181 0.218 0.118 0.995 6 5.9 15292
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.16 100 1.644 1.966 1.063 0.146 1.1 6.3
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 FREE R-VALUE 2.1 36.246 15264 750 94.89 0.237 0.2338 0.2345 0.2995 0.2979 50.11
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] -1.08 -0.54 -1.08 3.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.194 r_dihedral_angle_3_deg 17.159 r_lrange_it 16.937 r_dihedral_angle_6_deg 14.558 r_scangle_it 13.292 r_mcangle_it 10.822 r_scbond_it 9.567 r_dihedral_angle_1_deg 8.421 r_mcbond_it 7.556 r_angle_refined_deg 2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.194 r_dihedral_angle_3_deg 17.159 r_lrange_it 16.937 r_dihedral_angle_6_deg 14.558 r_scangle_it 13.292 r_mcangle_it 10.822 r_scbond_it 9.567 r_dihedral_angle_1_deg 8.421 r_mcbond_it 7.556 r_angle_refined_deg 2.72 r_nbtor_refined 0.293 r_symmetry_nbd_refined 0.272 r_nbd_refined 0.196 r_chiral_restr 0.179 r_symmetry_xyhbond_nbd_refined 0.173 r_xyhbond_nbd_refined 0.145 r_ncsr_local_group_1 0.139 r_gen_planes_refined 0.013 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1825 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction Aimless data scaling PHASER phasing