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Programmed cell death 1 ligand 1 with small molecule inhibitor ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9ERY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2MMagnesium chloride hexahydrate 0.1MBis-Tris 5.525% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.85 56.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.968 α = 90 b = 74.968 β = 90 c = 94.1 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 EIGER2 X 16M 2025-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
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 2.9 94.1 100 0.455 0.482 0.159 0.995 7.7 16.8 7143
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) 2.9 3.08 100 5.713 6.047 1.978 0.38 1.1 17.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.901 53.439 7119 334 99.986 0.216 0.2123 0.2126 0.2879 0.2894 RANDOM 92.186
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] -0.984 -0.492 -0.984 3.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.151 r_lrange_it 19.978 r_dihedral_angle_3_deg 18.861 r_scangle_it 16.187 r_dihedral_angle_6_deg 14.643 r_mcangle_it 12.603 r_scbond_it 10.696 r_dihedral_angle_1_deg 9.404 r_mcbond_it 8.182 r_angle_refined_deg 2.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.151 r_lrange_it 19.978 r_dihedral_angle_3_deg 18.861 r_scangle_it 16.187 r_dihedral_angle_6_deg 14.643 r_mcangle_it 12.603 r_scbond_it 10.696 r_dihedral_angle_1_deg 9.404 r_mcbond_it 8.182 r_angle_refined_deg 2.344 r_nbtor_refined 0.285 r_xyhbond_nbd_refined 0.223 r_ncsr_local_group_1 0.196 r_symmetry_nbd_refined 0.185 r_nbd_refined 0.182 r_chiral_restr 0.16 r_symmetry_xyhbond_nbd_refined 0.103 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1818 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 41
Software Software Software Name Purpose Aimless data scaling gemmi data extraction REFMAC refinement Aimless data scaling gemmi data extraction REFMAC refinement