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Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with 2-amino-1,3-benzothiazol-6-ol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9F2G Chains A, B, C, D, E, F, G and H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 PEG 3350 38%, 0.1 M Tris pH 8.5, 50 mM ammonium sulfate and 1 mM InsP6.
Protein:precipitant ratio 1:1.
Protein concentration: 16.5 mg/ml.
Protein buffer: 20 mM Tris pH 8.0 and 150 mM NaCl.
Soaking 2 weeks with saturated concentration of riluzole-like compound in PEG 3350 40%, 0.1 M Tris pH 8.5, 50 mM ammonium sulfate, 1 mM InsP6 condition.
Crystal Properties Matthews coefficient Solvent content 2.27 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.523 α = 90 b = 45.935 β = 93.79 c = 110.012 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 PILATUS3 2M KB mirror, elliptical beam shape 2021-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
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 1.45 109.77 99.8 0.064 0.988 7 4.4 165420 16.766
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 1.45 1.47 98.2 0.475 0.618 1.5 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.45 109.77 157236 8168 99.74 0.18679 0.18536 0.21389 0.2448 RANDOM 19.114
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] -0.01 -0.35 0.58 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.636 r_dihedral_angle_2_deg 6.615 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 5.13 r_long_range_B_other 4.966 r_scangle_other 3.692 r_mcangle_it 2.417 r_mcangle_other 2.416 r_scbond_it 2.337 r_scbond_other 2.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.636 r_dihedral_angle_2_deg 6.615 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 5.13 r_long_range_B_other 4.966 r_scangle_other 3.692 r_mcangle_it 2.417 r_mcangle_other 2.416 r_scbond_it 2.337 r_scbond_other 2.336 r_mcbond_it 1.539 r_mcbond_other 1.539 r_angle_refined_deg 1.424 r_angle_other_deg 0.467 r_chiral_restr 0.07 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6974 Nucleic Acid Atoms Solvent Atoms 1012 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing Coot model building PDB_EXTRACT data extraction