☰ Navigation Tabs
small molecule inhibitor in complex with PD-L1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P1O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1MBis-Tris 6.520% w/v PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 2.14 42.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.521 α = 90 b = 74.996 β = 95.49 c = 74.614 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS3 S 6M 2022-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.75 47.62 99 0.04 0.056 0.038 0.999 13.4 3.4 73948
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.78 98.7 0.955 1.299 0.875 0.543 1.2 3.2
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 1.75 47.62 73921 3656 98.847 0.246 0.2443 0.2445 0.2702 0.2713 36.555
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] -0.482 -2.074 1.077 -0.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.914 r_dihedral_angle_6_deg 15.632 r_dihedral_angle_3_deg 13.525 r_lrange_it 9.343 r_dihedral_angle_1_deg 7.69 r_scangle_it 7.201 r_mcangle_it 5.541 r_scbond_it 5.244 r_mcbond_it 4.002 r_angle_refined_deg 2.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.914 r_dihedral_angle_6_deg 15.632 r_dihedral_angle_3_deg 13.525 r_lrange_it 9.343 r_dihedral_angle_1_deg 7.69 r_scangle_it 7.201 r_mcangle_it 5.541 r_scbond_it 5.244 r_mcbond_it 4.002 r_angle_refined_deg 2.185 r_nbtor_refined 0.292 r_symmetry_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.201 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.145 r_ncsr_local_group_3 0.123 r_ncsr_local_group_14 0.123 r_ncsr_local_group_13 0.121 r_ncsr_local_group_10 0.119 r_ncsr_local_group_5 0.111 r_ncsr_local_group_1 0.106 r_ncsr_local_group_2 0.106 r_ncsr_local_group_7 0.102 r_ncsr_local_group_12 0.102 r_ncsr_local_group_9 0.098 r_ncsr_local_group_11 0.098 r_ncsr_local_group_15 0.098 r_ncsr_local_group_4 0.097 r_ncsr_local_group_8 0.093 r_ncsr_local_group_6 0.092 r_gen_planes_refined 0.011 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5580 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing