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Structure of HLA-A*02:01 in complex with NY-ESO-1 peptide and PA2.1 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S9X 1S9X, 3HC0 experimental model PDB 3HC0 1S9X, 3HC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2M L-Proline, 0.1M HEPES pH 7.5, 13% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.12 60.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.8 α = 90 b = 148.79 β = 90 c = 199.57 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 PILATUS 6M 2022-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.980 SSRL BL12-2
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 2.9 49.6 99.12 0.99 7.19 6.7 145809 76.85
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 2.9 3.01 95.2 0.381 0.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1S9X, 3HC0 2.9 49.59 1.33 145809 3749 98.2 0.2406 0.2394 0.2386 0.2844 0.2846 91.2
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 15.3425 f_angle_d 1.1786 f_chiral_restr 0.0622 f_plane_restr 0.0097 f_bond_d 0.0094
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19374 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose Coot model building PHENIX refinement PHASER phasing XDS data reduction Aimless data scaling