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Crystal structure of PD-L1 from P. dioica in complex with adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.16M sodium acetate trihydrate, 0.1M sodium cacodylate, 24% PEG8000, 3mM Adenine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.81 31.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.323 α = 90 b = 32.159 β = 128.29 c = 112.295 γ = 90
Symmetry Space Group C 1 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 100 CCD MAR CCD 165 mm 2009-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 1.65 30 92.8 0.09 6.7 4.2 61167 56763
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) 1.65 1.69 85.3 0.07 2 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3h5k 1.65 9.97 48429 41131 2167 84.93 0.214 0.214 0.213 0.2273 0.249 0.2512 RANDOM 16.817
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] 0.04 0.05 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.214 r_dihedral_angle_4_deg 25.509 r_dihedral_angle_3_deg 13.841 r_dihedral_angle_1_deg 6.99 r_scangle_it 3.397 r_angle_refined_deg 2.604 r_scbond_it 2.134 r_mcangle_it 1.633 r_mcbond_it 0.957 r_nbtor_refined 0.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.214 r_dihedral_angle_4_deg 25.509 r_dihedral_angle_3_deg 13.841 r_dihedral_angle_1_deg 6.99 r_scangle_it 3.397 r_angle_refined_deg 2.604 r_scbond_it 2.134 r_mcangle_it 1.633 r_mcbond_it 0.957 r_nbtor_refined 0.383 r_nbd_refined 0.303 r_symmetry_vdw_refined 0.297 r_xyhbond_nbd_refined 0.264 r_symmetry_hbond_refined 0.264 r_chiral_restr 0.117 r_bond_refined_d 0.037 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4100 Nucleic Acid Atoms Solvent Atoms 659 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data collection Il model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling Il phasing