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HLA-E*01:03 in complex with SARS-CoV-2 Omicron Nsp13 peptide, VIPLSAPTL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.15 M DL malic acid and 20% w/v of PEG3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.233 α = 90 b = 66.53 β = 95.256 c = 158.446 γ = 90
Symmetry Space Group C 1 2 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 2023-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97625 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.87 47.95 99.8 0.12 0.142 0.997 10.5 2 104376
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 1.87 1.9 0.847 0.525 0.73 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.872 47.95 104345 5251 99.66 0.18 0.178 0.1875 0.2197 0.2271 23.697
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] -0.64 -0.5 0.183 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.344 r_dihedral_angle_3_deg 12.974 r_dihedral_angle_2_deg 7.442 r_dihedral_angle_1_deg 6.812 r_lrange_it 6.802 r_lrange_other 6.717 r_scangle_it 4.947 r_scangle_other 4.947 r_mcangle_it 3.187 r_mcangle_other 3.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.344 r_dihedral_angle_3_deg 12.974 r_dihedral_angle_2_deg 7.442 r_dihedral_angle_1_deg 6.812 r_lrange_it 6.802 r_lrange_other 6.717 r_scangle_it 4.947 r_scangle_other 4.947 r_mcangle_it 3.187 r_mcangle_other 3.187 r_scbond_it 3.023 r_scbond_other 3.023 r_mcbond_it 2.022 r_mcbond_other 2.022 r_angle_refined_deg 1.434 r_angle_other_deg 0.52 r_nbd_refined 0.201 r_symmetry_nbd_refined 0.196 r_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.176 r_nbd_other 0.172 r_symmetry_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.066 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9348 Nucleic Acid Atoms Solvent Atoms 1069 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing Coot model building