☰ Navigation Tabs
Structure of SARS-CoV-2 NSP14 bound to N-((4-vinylthiazol-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 277.15 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 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.755 α = 90 b = 68.728 β = 90 c = 138.245 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 2023-02-17 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 68.73 99.45 0.14449 0.1512 0.04248 0.996 10.19 11.8 29237 34.77
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 97.67 0.4845 0.816 1.16
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 61.54 1.34 29235 2002 99.44 0.213 0.2111 0.2114 0.2398 0.2399 38.68
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 9.0525 f_angle_d 1.2753 f_chiral_restr 0.0661 f_bond_d 0.0137 f_plane_restr 0.0124
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3467 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement DIALS data reduction xia2 data scaling PHASER phasing