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Crystal structure of HLA B*18:01 in complex with YERMCNIL, an 8-mer epitope from Influenza A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Potassium Nitrate, 20% w/v PEG 3350 at pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.58 52.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.853 α = 90 b = 81.482 β = 90 c = 111.3 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 EIGER X 16M 2023-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953732 Australian Synchrotron MX2
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 1.4 46.25 99.6 0.999 15.6 7.9 91186 11.59
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 1.4 1.42 0.639 3.3
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 1.4 40.74 1.35 91097 4601 99.51 0.1554 0.1536 0.1582 0.1886 0.1917 17.91
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 13.7625 f_angle_d 1.0268 f_chiral_restr 0.0939 f_plane_restr 0.0101 f_bond_d 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3147 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing