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Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp3 epitope (orf1ab)1350-1364
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.1 M SPG pH 4.6, 25 % PEG1500
Crystal Properties Matthews coefficient Solvent content 3.2 61.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.23 α = 90 b = 95.49 β = 90 c = 202.43 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 EIGER2 XE 16M 2021-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.2 55.11 99.9 0.345 0.35100000000000003 0.0663 0.998 9.39 27.9 60213 44.49
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 2.2 2.28 98.89 4.163 4.244 0.818 0.517 0.86
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 2.2 55.11 1.33 60029 2972 99.64 0.2088 0.2072 0.2076 0.2397 0.2399 62.96
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 14.4065 f_angle_d 0.8163 f_chiral_restr 0.0538 f_plane_restr 0.0068 f_bond_d 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6336 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing