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Structure of FabS1CE2_P4a 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 5.5 295 20% PEG1500 0.1M Sodium Citrate pH 5.5, cryoprotected in this solution plus 30% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.62 α = 90 b = 72.27 β = 117.51 c = 72.522 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 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 0.919921 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 1.64 34.8 100 0.153 0.166 0.062 0.996 6.6 7 77525 17.78
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 1.64 1.73 100 2.406 2.614 1.007 0.461 0.7 6.6
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 1.64 34.8 1.35 64582 3200 82.69 0.1759 0.1743 0.1726 0.2073 0.2053 22.86
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 16.0735 f_angle_d 0.8827 f_chiral_restr 0.0598 f_bond_d 0.0071 f_plane_restr 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4213 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms 139
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing