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Human Class I MHC HLA-A2 bound to sorting nexin 24 (127-135) neoantigen KLSHQLVLL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals were harvested and cryoprotected in 8% glycerol/92% mother liquor and immediately stored in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.33 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.196 α = 90 b = 85.432 β = 90.01 c = 84.075 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 16M 2021-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
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 2.87 59.92 98.56 0.1708 0.2049 0.1116 0.947 5.16 3.3 18717
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.87 2.973 0.2445
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.87 59.92 1.39 18706 98.56 0.1999 0.1992 0.2454 0.245
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 8.771 f_angle_d 0.888 f_chiral_restr 0.05 f_plane_restr 0.013 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6316 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing