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Crystal structure of SARS-CoV-2 nsp14 with SAH and GpppA bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 293 5.1% (w/v) PEG 10000
2.3% (v/v) 1,3-butanediol
0.2 M DL-malate-imidazole
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.1 α = 90 b = 99.472 β = 109.29 c = 90.515 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 2021-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.26 85.43 87.4 0.024 0.999 16.3 7 32680
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 2.26 2.54 61.4 0.477 0.563 1.4 6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.257 85.43 32680 1524 61.9 0.2352 0.2337 0.2279 0.2656 0.2688 RANDOM 80.29
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] -1.8796 5.1163 -0.8097 2.6893
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.39 t_omega_torsion 2.92 t_angle_deg 0.9 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_utility_distance t_utility_angle
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.39 t_omega_torsion 2.92 t_angle_deg 0.9 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_utility_distance t_utility_angle t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6562 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 169
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing BUSTER refinement