☰ Navigation Tabs
1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer from SARS-CoV-2 in Complex with Sinefungin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W75 PDB entry 6W75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 5.3 mg/mL 1:1 nsp10/nsp16 in 0.15 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen F10 (0.4 M potassium/sodium tartrate), soak and cryoprotection: 5 mM SFG, 4 M sodium formate, 3 hrs
Crystal Properties Matthews coefficient Solvent content 3.95 68.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.247 α = 90 b = 166.247 β = 90 c = 98.139 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 1.98 30 100 0.071 0.071 0.078 0.033 22.2 5.5 108598 -3 31.7
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 1.98 2.01 100 0.784 0.784 0.874 0.384 0.724 2 5.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 6W75 1.98 29.922 108429 5357 99.96 0.163 0.1623 0.1689 0.1799 0.1879 38.118
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] 0.283 0.141 0.283 -0.917
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.641 r_dihedral_angle_3_deg 8.057 r_lrange_it 6.904 r_lrange_other 6.735 r_dihedral_angle_4_deg 5.649 r_scangle_it 3.46 r_scangle_other 3.46 r_mcangle_it 2.656 r_mcangle_other 2.655 r_dihedral_angle_1_deg 2.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.641 r_dihedral_angle_3_deg 8.057 r_lrange_it 6.904 r_lrange_other 6.735 r_dihedral_angle_4_deg 5.649 r_scangle_it 3.46 r_scangle_other 3.46 r_mcangle_it 2.656 r_mcangle_other 2.655 r_dihedral_angle_1_deg 2.463 r_scbond_it 2.34 r_scbond_other 2.327 r_mcbond_it 1.603 r_mcbond_other 1.603 r_dihedral_angle_other_3_deg 1.44 r_angle_refined_deg 1.342 r_angle_other_deg 0.347 r_nbd_other 0.223 r_nbd_refined 0.2 r_symmetry_xyhbond_nbd_refined 0.177 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.171 r_symmetry_nbd_refined 0.137 r_xyhbond_nbd_refined 0.121 r_metal_ion_refined 0.121 r_symmetry_nbtor_other 0.096 r_chiral_restr 0.06 r_gen_planes_refined 0.055 r_gen_planes_other 0.051 r_symmetry_xyhbond_nbd_other 0.01 r_bond_refined_d 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6408 Nucleic Acid Atoms Solvent Atoms 636 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing