☰ Navigation Tabs
Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1) and S-Adenosyl-L-homocysteine (SAH).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W4H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 292 Protein: 4.7mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol;
Screen: Anions (E6), 0.1M Sodium acetate pH 4.6, 0.5M Sodium succinate;
Soak: 17 hours, 0.2mM [M7Gppp]rArUrUrArArA, 5mM SAM, 5mM Manganese chloride,
Cryo: 4M Sodium formate.
Crystal Properties Matthews coefficient Solvent content 3.92 68.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.238 α = 90 b = 167.238 β = 90 c = 98.867 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 2020-08-07 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 2.15 50 100 0.09 0.09 0.097 0.036 26.6 7.1 86204 -3 42.2
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 2.15 2.19 100 1.239 1.239 1.335 0.493 0.735 1.8 7.1
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 6w4h 2.15 30 81799 4338 99.81 0.1745 0.1733 0.1791 0.1981 0.2016 RANDOM 55.875
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] 1.29 0.65 1.29 -4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.651 r_dihedral_angle_3_deg 9 r_dihedral_angle_4_deg 8.747 r_dihedral_angle_1_deg 2.788 r_angle_refined_deg 1.344 r_angle_other_deg 0.381 r_chiral_restr 0.06 r_gen_planes_refined 0.053 r_gen_planes_other 0.047 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.651 r_dihedral_angle_3_deg 9 r_dihedral_angle_4_deg 8.747 r_dihedral_angle_1_deg 2.788 r_angle_refined_deg 1.344 r_angle_other_deg 0.381 r_chiral_restr 0.06 r_gen_planes_refined 0.053 r_gen_planes_other 0.047 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6496 Nucleic Acid Atoms 188 Solvent Atoms 398 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing