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HLA-E*01:03 in complex with SARS-CoV-2 Nsp13 peptide, VMPLSAPTL
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 potassium bromide, 20% w/v of PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.33 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.493 α = 90 b = 67.597 β = 92.78 c = 152.228 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) 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 1.71 46.11 99.9 0.07 0.083 0.044 0.999 11.7 2 132063
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 1.71 1.74 100 1.252 0.774 0.628 1.4
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 1.71 46.11 131954 6698 99.84 0.205 0.2036 0.2114 0.2433 0.2475 32.334
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] -0.74 -1.244 0.863 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.271 r_dihedral_angle_6_deg 14.229 r_dihedral_angle_2_deg 8.462 r_lrange_it 7.5 r_lrange_other 7.457 r_dihedral_angle_1_deg 6.853 r_scangle_it 5.813 r_scangle_other 5.813 r_mcangle_it 3.947 r_mcangle_other 3.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.271 r_dihedral_angle_6_deg 14.229 r_dihedral_angle_2_deg 8.462 r_lrange_it 7.5 r_lrange_other 7.457 r_dihedral_angle_1_deg 6.853 r_scangle_it 5.813 r_scangle_other 5.813 r_mcangle_it 3.947 r_mcangle_other 3.946 r_scbond_it 3.642 r_scbond_other 3.641 r_mcbond_it 2.701 r_mcbond_other 2.701 r_angle_refined_deg 1.469 r_angle_other_deg 0.537 r_symmetry_nbd_refined 0.262 r_nbd_other 0.226 r_xyhbond_nbd_refined 0.21 r_nbd_refined 0.208 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.139 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.014 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9353 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing Coot model building