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Structure of SARS-CoV-2 NSP14 bound to N-((4-cyclopropylthiazol-2-yl)methyl)-1H-pyrazole-3-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5SKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Crystals appeared after two weeks when mixed 1:1 ratio with mother liquor containing sodium phosphate monobasic (1.26M to 1.61M) and potassium phosphate dibasic (0.14M to 0.24M). Ligand was soaked for at least 1 hour at a final concentration between 10-50 mM (10% DMSO).
Crystal Properties Matthews coefficient Solvent content 2.69 54.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.727 α = 90 b = 68.427 β = 90 c = 138.082 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 80 PIXEL DECTRIS EIGER X 9M 2023-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97857 APS 21-ID-F
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 2.3 60.81 98.88 0.0839 0.08802 0.02615 0.998 20.36 11.1 28946 32.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 99.89 0.118 0.981 7.39
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 2.3 60.81 1.34 28919 1447 98.89 0.2075 0.2062 0.2089 0.2311 0.2332 36.87
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 7.3122 f_angle_d 0.7148 f_chiral_restr 0.0454 f_plane_restr 0.0063 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3352 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement DIALS data reduction xia2 data scaling PHASER phasing