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Complex of PD-L1 with VHH6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1 M HEPES:MOPS, pH 7.5, 0.02 M Ammonium acetate, 0.02 M Potassium sodium tartrate tetrahydrate, 0.02 M Sodium citrate tribasic dihydrate, 0.02 M Sodium formate, 0.02M Sodium oxamate,
10% (w/v) PEG 20000 and 20% (v/v) PEG 500-MME.
Crystal Properties Matthews coefficient Solvent content 3.9 68.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.575 α = 90 b = 99.575 β = 90 c = 171.515 γ = 90
Symmetry Space Group I 41 2 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 PILATUS3 2M 2022-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
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 1.6 43.1 99.9 0.055 0.067 0.038 0.999 15.5 5.6 56912
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 1.6 1.63 1.119 1.369 0.777 0.536 5.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3BIS 1.6 43.094 56884 2852 99.83 0.163 0.1623 0.1615 0.1846 0.1829 25.702
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] 0.435 0.435 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.654 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 13.431 r_lrange_other 7.433 r_lrange_it 7.431 r_dihedral_angle_1_deg 7.017 r_scangle_it 5.586 r_scangle_other 5.585 r_dihedral_angle_other_2_deg 4.944 r_scbond_other 3.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.654 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 13.431 r_lrange_other 7.433 r_lrange_it 7.431 r_dihedral_angle_1_deg 7.017 r_scangle_it 5.586 r_scangle_other 5.585 r_dihedral_angle_other_2_deg 4.944 r_scbond_other 3.958 r_scbond_it 3.957 r_mcangle_other 3.347 r_mcangle_it 3.342 r_mcbond_it 2.482 r_mcbond_other 2.481 r_angle_other_deg 2.391 r_angle_refined_deg 2.138 r_nbd_other 0.321 r_symmetry_xyhbond_nbd_refined 0.318 r_symmetry_nbd_refined 0.236 r_symmetry_nbd_other 0.231 r_xyhbond_nbd_refined 0.211 r_nbd_refined 0.193 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_other 0.101 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.091 r_xyhbond_nbd_other 0.072 r_bond_other_d 0.035 r_bond_refined_d 0.018 r_gen_planes_other 0.017 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1903 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing