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Structure of FabS1CE2_P2a in complex with the N-terminal domain of PD-L1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VUC experimental model PDB 8VUC experimental model PDB 5C3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 295 5.5M Sodium Formate, 0.1M Sodium Acetate trihydrate pH4.6, final pH 5.8, cryoprotected in paratone oil
Crystal Properties Matthews coefficient Solvent content 3.34 63.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.358 α = 90 b = 239.679 β = 90 c = 104.282 γ = 90
Symmetry Space Group C 2 2 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 9M mirrors 2026-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97935 NSLS-II 17-ID-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 1.97 40.412 90.9 0.235 0.266 0.122 0.995 8.3 8.8 27786 28.59
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 1.97 2.282 74.2 1.879 2.095 0.922 0.213 1.4 8.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.22 40.41 1.34 26827 1324 64.54 0.2007 0.1987 0.2 0.2386 0.2387 33.32
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.2002 f_angle_d 1.0643 f_chiral_restr 0.0589 f_plane_restr 0.0102 f_bond_d 0.0093
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4182 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing