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Co-crystal structure of human PD-L1 complexed with Compound A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM NaCitrate, pH 6.5 and 22% (w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 3.86 68.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.003 α = 90 b = 172.173 β = 90 c = 80.585 γ = 90
Symmetry Space Group C 2 2 21
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 2018-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97928 ALBA XALOC
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 2.49 80.58 99.1 0.097 0.104 0.038 0.998 14.6 7.3 24239
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) 1 2.49 2.62 99.1 1.163 1.246 0.443 0.711 7.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ZQK 2.49 58.9 23114 1117 98.78 0.1791 0.1767 0.1847 0.228 0.2273 RANDOM 53.871
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] -3.24 -1.87 5.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.916 r_dihedral_angle_4_deg 27.13 r_dihedral_angle_3_deg 20.813 r_dihedral_angle_1_deg 6.585 r_angle_refined_deg 1.663 r_angle_other_deg 1.378 r_chiral_restr 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.916 r_dihedral_angle_4_deg 27.13 r_dihedral_angle_3_deg 20.813 r_dihedral_angle_1_deg 6.585 r_angle_refined_deg 1.663 r_angle_other_deg 1.378 r_chiral_restr 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2912 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 63
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing