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Dimeric Structure of PD-L1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BIS PDB ENTRY 3BIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 15% PEG 3350 (w/v), 0.2M ammonium acetate (NH4Ac), 0.1M BIS-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.865 α = 90 b = 91.373 β = 90 c = 140.316 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE RIGAKU RAXIS IV++ 2008-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 50 91.1 5.7 36104 19603 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.7 98.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 3BIS 2.7 15 2 12011 645 97.62 0.22908 0.22567 0.2229 0.29614 0.2902 RANDOM 58.811
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] 1.8 -4.59 2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.277 r_dihedral_angle_3_deg 21.309 r_dihedral_angle_4_deg 17.326 r_dihedral_angle_1_deg 7.416 r_scangle_it 2.595 r_angle_refined_deg 1.734 r_scbond_it 1.686 r_mcangle_it 1.316 r_mcbond_it 0.742 r_symmetry_hbond_refined 0.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.277 r_dihedral_angle_3_deg 21.309 r_dihedral_angle_4_deg 17.326 r_dihedral_angle_1_deg 7.416 r_scangle_it 2.595 r_angle_refined_deg 1.734 r_scbond_it 1.686 r_mcangle_it 1.316 r_mcbond_it 0.742 r_symmetry_hbond_refined 0.352 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.254 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.116 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3428 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling