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Crystal structure of SARS-CoV-2 NSP14 in complex with compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7R2V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 7% isopropanol and 0.1 M imidazole, pH 7.75
Crystal Properties Matthews coefficient Solvent content 2.49 50.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.587 α = 90 b = 101.864 β = 108.86 c = 91.018 γ = 90
Symmetry Space Group P 1 21 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 2022-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.85 63.96 97.5 0.089 0.102 0.05 0.998 12.3 4.1 26758 72.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.9 1.031 1.165 0.536 0.556 1.4
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 2.85 63.96 1.34 25872 622 94.27 0.2322 0.231 0.2277 0.283 0.279 77.08
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 13.171 f_angle_d 1.7225 f_chiral_restr 0.0861 f_bond_d 0.0139 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7002 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing