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Co-crystal structure of PD-L1 with low molecular weight inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.2 M S38 sodium citrate tribasic dihydrate 0.01 M sodium borate, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.45 α = 90 b = 73.45 β = 90 c = 96.08 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 PILATUS3 6M 2023-01-25 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) 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 3.31 48.04 99.9 0.997 9.39 10.55 4743
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.31 3.51 0.423 0.96
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 3.312 38.336 4743 224 99.853 0.237 0.2343 0.234 0.2971 0.2965 97.907
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] -0.052 -0.026 -0.052 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.785 r_dihedral_angle_6_deg 17.618 r_lrange_it 17.117 r_lrange_other 17.116 r_dihedral_angle_2_deg 16.027 r_mcangle_it 11.053 r_mcangle_other 11.049 r_scangle_it 10.814 r_scangle_other 10.81 r_dihedral_angle_1_deg 8.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.785 r_dihedral_angle_6_deg 17.618 r_lrange_it 17.117 r_lrange_other 17.116 r_dihedral_angle_2_deg 16.027 r_mcangle_it 11.053 r_mcangle_other 11.049 r_scangle_it 10.814 r_scangle_other 10.81 r_dihedral_angle_1_deg 8.334 r_mcbond_it 6.951 r_mcbond_other 6.951 r_scbond_it 6.747 r_scbond_other 6.745 r_angle_refined_deg 1.744 r_angle_other_deg 0.803 r_symmetry_xyhbond_nbd_other 0.365 r_nbd_other 0.323 r_symmetry_xyhbond_nbd_refined 0.315 r_xyhbond_nbd_refined 0.308 r_symmetry_nbd_refined 0.262 r_chiral_restr_other 0.236 r_nbd_refined 0.198 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.171 r_ncsr_local_group_1 0.151 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.085 r_xyhbond_nbd_other 0.036 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1765 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing