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Crystal structure of HLA-A*03:01 in complex with a wild-type PIK3CA peptide analogue (Trp-6 Bta)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L1C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 15% w/v Polyethylene glycol 6,000, 50 mM Potassium chloride; 10 mM Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.39 63.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.095 α = 90 b = 156.095 β = 90 c = 85.715 γ = 120
Symmetry Space Group P 6 2 2
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 2022-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-ID
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 1.77 43.89 98.37 0.1813 0.1836 0.02909 0.996 23.49 38.2 60123 17.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.833 1.638 0.2765 0.779 5.34
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 1.77 43.89 0.17 59188 3954 98.13 0.2059 0.2036 0.2033 0.2375 0.2371 30.41
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 14.8816 f_angle_d 0.8784 f_chiral_restr 0.0535 f_plane_restr 0.0075 f_bond_d 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3123 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing