☰ Navigation Tabs
Crystal Structure of human Programmed cell death 1 ligand 1 (PD-L1) bound to Small molecule inhibitor Compound-10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NIU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 299 0.1M Tris pH 8.5, 0.1M Magnesium chloride, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.36 47.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.717 α = 90 b = 85.206 β = 90 c = 161.157 γ = 90
Symmetry Space Group P 21 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 EIGER X 16M 2022-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953732 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.05 45.44 100 0.999 24.6 13.2 36207
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.11 0.958
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.05 45.44 36139 1802 99.964 0.233 0.2311 0.2359 0.2601 0.265 48.133
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] 1.157 -0.911 -0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.813 r_dihedral_angle_4_deg 16.03 r_dihedral_angle_3_deg 13.486 r_lrange_it 7.262 r_lrange_other 7.248 r_dihedral_angle_1_deg 6.949 r_scangle_it 2.985 r_scangle_other 2.985 r_mcangle_it 2.706 r_mcangle_other 2.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.813 r_dihedral_angle_4_deg 16.03 r_dihedral_angle_3_deg 13.486 r_lrange_it 7.262 r_lrange_other 7.248 r_dihedral_angle_1_deg 6.949 r_scangle_it 2.985 r_scangle_other 2.985 r_mcangle_it 2.706 r_mcangle_other 2.706 r_scbond_it 1.868 r_scbond_other 1.868 r_mcbond_it 1.678 r_mcbond_other 1.678 r_angle_refined_deg 1.504 r_angle_other_deg 1.318 r_symmetry_xyhbond_nbd_refined 0.287 r_nbd_other 0.23 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.204 r_symmetry_nbd_refined 0.183 r_ncsr_local_group_4 0.174 r_nbtor_refined 0.169 r_ncsr_local_group_6 0.169 r_ncsr_local_group_1 0.158 r_ncsr_local_group_3 0.154 r_ncsr_local_group_5 0.154 r_ncsr_local_group_2 0.151 r_symmetry_xyhbond_nbd_other 0.131 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_chiral_restr_other 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4032 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing