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Solubilizer tag effect on PD-L1/inhibitor binding properties for m-terphenyl derivatives
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 27 % w/v PEG 3350, 0.1 M Bis-Tris propane, pH 7.0 and 0.2 M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.088 α = 90 b = 109.991 β = 90 c = 51.823 γ = 90
Symmetry Space Group P 21 21 2
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 2021-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 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 2.17 46.88 99.7 0.144 0.173 0.094 0.993 6.8 6 16333
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 2.17 2.24 0.762 0.905 0.484 0.734 6.3
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 2.17 46.88 16297 865 99.597 0.272 0.2708 0.2708 0.2894 0.2894 35.683
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] 0.169 -0.013 -0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.464 r_lrange_it 11.574 r_dihedral_angle_3_deg 11.308 r_dihedral_angle_2_deg 8.859 r_scangle_it 7.622 r_dihedral_angle_1_deg 5.91 r_mcangle_it 5.508 r_scbond_it 5.299 r_mcbond_it 3.837 r_angle_refined_deg 0.983
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.464 r_lrange_it 11.574 r_dihedral_angle_3_deg 11.308 r_dihedral_angle_2_deg 8.859 r_scangle_it 7.622 r_dihedral_angle_1_deg 5.91 r_mcangle_it 5.508 r_scbond_it 5.299 r_mcbond_it 3.837 r_angle_refined_deg 0.983 r_nbtor_refined 0.305 r_symmetry_nbd_refined 0.234 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.1 r_chiral_restr 0.05 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2024 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing