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Structure of human PD-L1 in complex with macrocyclic inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.24 298 0.1M sodium citrate 1.95M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 3.57 65.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.47 α = 90 b = 86.47 β = 90 c = 86.47 γ = 90
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 PILATUS3 6M 2021-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.663 86.47 100 0.091 0.092 0.017 18.1 27.7 17309 17309
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 1.576 1.576 1.605 0.301 0.5 28.2
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5O45 1.9 61.22 16436 873 99.99 0.2331 0.2324 0.2465 0.2566 RANDOM 62.919
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.082 r_dihedral_angle_4_deg 26.596 r_dihedral_angle_3_deg 18.412 r_dihedral_angle_1_deg 8.946 r_angle_refined_deg 2.262 r_angle_other_deg 1.466 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.082 r_dihedral_angle_4_deg 26.596 r_dihedral_angle_3_deg 18.412 r_dihedral_angle_1_deg 8.946 r_angle_refined_deg 2.262 r_angle_other_deg 1.466 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1037 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing