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Structure of the complex of human programmed death-1 (PD-1) and its ligand PD-L1.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BIK chain A -3BIK, chain B 3RRQ experimental model PDB 3RRQ chain A -3BIK, chain B 3RRQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 0.1 M BIS-Tris pH 5.5, 1.84 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.32 62.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.862 α = 90 b = 70.862 β = 90 c = 114.367 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 193 PIXEL DECTRIS PILATUS 6M 2015-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91843 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.45 61.37 99.98 0.043 35.22 10.6 12737
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 99.92 0.48 5.21 11.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT chain A -3BIK, chain B 3RRQ 2.45 61.37 12082 625 99.89 0.2092 0.2071 0.2114 0.2527 0.2558 RANDOM 57.568
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] -0.72 -0.36 -0.72 2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.544 r_dihedral_angle_3_deg 17.366 r_dihedral_angle_4_deg 12.728 r_dihedral_angle_1_deg 7.67 r_mcangle_it 4.885 r_mcbond_other 3.233 r_mcbond_it 3.231 r_angle_refined_deg 1.768 r_angle_other_deg 0.86 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.544 r_dihedral_angle_3_deg 17.366 r_dihedral_angle_4_deg 12.728 r_dihedral_angle_1_deg 7.67 r_mcangle_it 4.885 r_mcbond_other 3.233 r_mcbond_it 3.231 r_angle_refined_deg 1.768 r_angle_other_deg 0.86 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1650 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 1
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction