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Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VWW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 BewuA.18928.a.MX151.PW38806 at 36 mg/ml mixed 1:1 with Morpheus(G3): 10% (w/v) PEG 4000, 20% (v/v) glycerol, 0.1 M MES/imidazole, pH=6.5, 0.02 M of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium l-tartrate, sodium oxamate. Tray: 315968g8, puck: teq6-3.
Crystal Properties Matthews coefficient Solvent content 4.46 72.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.82 α = 90 b = 150.82 β = 90 c = 112.57 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 Beryllium Lenses 2020-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.35 50 100 0.077 0.081 0.999 22.57 11.456 60593 46.957
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.41 100 0.594 0.621 0.95 4.15 11.486
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6vww 2.35 45.21 1.35 60551 2078 99.97 0.1581 0.1572 0.1619 0.1825 0.1852 52.51
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 19.4244 f_angle_d 0.8012 f_chiral_restr 0.0547 f_bond_d 0.0066 f_plane_restr 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5450 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction