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Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IUS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M Sodium HEPES 7.5 25 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.753 α = 90 b = 75.405 β = 97.249 c = 75.923 γ = 90
Symmetry Space Group P 1 21 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 2023-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03322 PETRA III, DESY P11
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 2.5 48.39 99.2 0.148 0.174 0.091 0.997 6.9 7.1 27366
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 2.5 2.6 2.112 2.474 1.278 0.695 7.3
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 2.5 44.393 27351 1380 99.058 0.256 0.253 0.253 0.3025 0.3024 64.368
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] -0.536 -4.097 3.138 -1.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.965 r_dihedral_angle_3_deg 15.974 r_lrange_it 15.452 r_lrange_other 15.451 r_dihedral_angle_6_deg 14.879 r_scangle_it 9.655 r_scangle_other 9.612 r_mcangle_it 9.002 r_mcangle_other 9.002 r_dihedral_angle_1_deg 8.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.965 r_dihedral_angle_3_deg 15.974 r_lrange_it 15.452 r_lrange_other 15.451 r_dihedral_angle_6_deg 14.879 r_scangle_it 9.655 r_scangle_other 9.612 r_mcangle_it 9.002 r_mcangle_other 9.002 r_dihedral_angle_1_deg 8.056 r_scbond_it 6.071 r_scbond_other 6.045 r_mcbond_it 5.842 r_mcbond_other 5.818 r_angle_refined_deg 1.766 r_angle_other_deg 0.766 r_xyhbond_nbd_refined 0.349 r_symmetry_nbd_refined 0.216 r_nbd_refined 0.178 r_nbtor_refined 0.163 r_symmetry_nbd_other 0.159 r_nbd_other 0.157 r_ncsr_local_group_9 0.139 r_ncsr_local_group_14 0.137 r_ncsr_local_group_5 0.13 r_ncsr_local_group_8 0.127 r_ncsr_local_group_3 0.126 r_ncsr_local_group_12 0.126 r_ncsr_local_group_4 0.123 r_ncsr_local_group_13 0.122 r_ncsr_local_group_11 0.119 r_ncsr_local_group_2 0.113 r_ncsr_local_group_15 0.112 r_ncsr_local_group_7 0.109 r_ncsr_local_group_6 0.101 r_ncsr_local_group_1 0.099 r_chiral_restr 0.097 r_symmetry_xyhbond_nbd_refined 0.093 r_ncsr_local_group_10 0.089 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.072 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5655 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing