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Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.2 M ammonium formate and 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.313 α = 90 b = 55.182 β = 90 c = 141.773 γ = 90
Symmetry Space Group P 2 21 21
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 6M 2015-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 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 2.3 47.26 99.9 0.093 12.4 6.8 12626
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5c3t 2.3 47.26 11974 610 99.84 0.2445 0.2412 0.3052 0.2854 RANDOM 44.112
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] 2.23 2.3 -4.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.254 r_dihedral_angle_4_deg 29.198 r_dihedral_angle_3_deg 17.24 r_dihedral_angle_1_deg 8.03 r_mcangle_it 4.759 r_mcbond_it 3.302 r_mcbond_other 3.301 r_angle_refined_deg 1.878 r_angle_other_deg 1.089 r_chiral_restr 0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.254 r_dihedral_angle_4_deg 29.198 r_dihedral_angle_3_deg 17.24 r_dihedral_angle_1_deg 8.03 r_mcangle_it 4.759 r_mcbond_it 3.302 r_mcbond_other 3.301 r_angle_refined_deg 1.878 r_angle_other_deg 1.089 r_chiral_restr 0.214 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1906 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 32
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing