☰ Navigation Tabs
Crystal structure of HLA B*13:01 in complex with SVLNDILARL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG3350 and 2% EG
Crystal Properties Matthews coefficient Solvent content 2.07 40.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.143 α = 90 b = 81.97 β = 90 c = 107.81 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 2022-07-30 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) 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 1.9 45.47 100 0.112 0.12 0.044 0.998 12.2 7.4 35846 22.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 0.804 0.864 0.313 0.818 2.8 7.6
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 1.9 45.47 1.35 35776 1809 99.94 0.1878 0.186 0.1867 0.2211 0.2209 26.86
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 14.7102 f_angle_d 0.8971 f_chiral_restr 0.0561 f_plane_restr 0.0081 f_bond_d 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3152 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing