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Crystal structure of HLA-A*11:01 bound to G12V-9-T2 peptide(VTGAVGVGK)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.1 M Imidazole pH 7.0, 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.81 56.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.381 α = 90 b = 67.187 β = 98.914 c = 76.446 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 EIGER2 S 9M 2024-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 50.2 100 0.078 0.039 0.999 11.3 4.9 54877 22.11
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 1.7 1.79 100 0.919 0.468 0.429 2 4.9
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 1.7 27.67 1.34 54714 2728 99.75 0.255 0.2533 0.2527 0.2864 0.2862 33.88
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 15.4055 f_angle_d 0.8485 f_chiral_restr 0.0528 f_plane_restr 0.0081 f_bond_d 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3120 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing Coot model building PHENIX refinement