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Crystal structure of PD-L1 complexed with a nanobody at 1.7 Angstron resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 295 2M NaCl, 1.4M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.13 α = 90 b = 83.13 β = 90 c = 73.23 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2016-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9777 SSRF BL19U1
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 1.7 51.34 99.9 9.6 6.9 31640
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.7 41.6 29996 1611 99.83 0.17969 0.17839 0.1865 0.20439 0.2104 RANDOM 25.983
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] 0.05 0.05 0.05 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.408 r_dihedral_angle_4_deg 17.879 r_dihedral_angle_3_deg 13.237 r_dihedral_angle_1_deg 6.74 r_long_range_B_refined 5.439 r_long_range_B_other 5.325 r_scangle_other 2.679 r_mcangle_it 2.024 r_mcangle_other 2.023 r_scbond_it 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.408 r_dihedral_angle_4_deg 17.879 r_dihedral_angle_3_deg 13.237 r_dihedral_angle_1_deg 6.74 r_long_range_B_refined 5.439 r_long_range_B_other 5.325 r_scangle_other 2.679 r_mcangle_it 2.024 r_mcangle_other 2.023 r_scbond_it 1.68 r_scbond_other 1.668 r_angle_refined_deg 1.455 r_mcbond_it 1.21 r_mcbond_other 1.21 r_angle_other_deg 0.718 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1879 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing