☰ Navigation Tabs
2.0 Angstrom Resolution Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with S-Adenosyl-L-Homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 Protein: 5.3 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol;
Screen: ComPAS (F10), 0.4M Potassium/Sodium tartrate;
Soak and Cryo: 5mM SAH, 4M Sodium formate, 3 hrs.
Crystal Properties Matthews coefficient Solvent content 3.98 69.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.917 α = 90 b = 166.917 β = 90 c = 98.099 γ = 120
Symmetry Space Group P 32 2 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 CCD MARMOSAIC 300 mm CCD Be 2020-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 30 100 0.101 0.101 0.11 0.044 16.7 6.5 105884 -3 34.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (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 2.03 100 0.795 0.795 0.866 0.34 0.933 3.2 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6w75 2 29.79 100620 5233 99.8 0.1721 0.1711 0.1764 0.1911 0.1939 RANDOM 40.744
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] 1.35 0.67 1.35 -4.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.92 r_dihedral_angle_3_deg 8.207 r_dihedral_angle_4_deg 6.1 r_dihedral_angle_1_deg 2.423 r_angle_refined_deg 1.33 r_angle_other_deg 0.344 r_chiral_restr 0.059 r_gen_planes_refined 0.055 r_gen_planes_other 0.051 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.92 r_dihedral_angle_3_deg 8.207 r_dihedral_angle_4_deg 6.1 r_dihedral_angle_1_deg 2.423 r_angle_refined_deg 1.33 r_angle_other_deg 0.344 r_chiral_restr 0.059 r_gen_planes_refined 0.055 r_gen_planes_other 0.051 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6400 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing