☰ Navigation Tabs
Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with riluzole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CE0 Chain A
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 o/n with saturated concentration of riluzole 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 2.12 42.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.056 α = 90 b = 43.383 β = 91.44 c = 109.326 γ = 90
Symmetry Space Group I 1 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 PIXEL DECTRIS EIGER2 X CdTe 16M Toroidal mirror, elliptical beam shape 2021-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.774899 ESRF ID23-1
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 1.3 46.56 97 0.026 0.999 12.3 5.5 103602 14.431
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 1.3 1.32 89.9 0.363 0.685 1.9 4.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.3 46.56 98450 5140 96.37 0.16856 0.1675 0.1764 0.18898 0.1957 RANDOM 17.108
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] 0.29 0.38 -0.23 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.081 r_dihedral_angle_2_deg 7.485 r_dihedral_angle_1_deg 6.531 r_long_range_B_refined 4.711 r_long_range_B_other 4.384 r_scangle_other 3.069 r_mcangle_it 2.066 r_mcangle_other 2.066 r_scbond_it 1.922 r_scbond_other 1.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.081 r_dihedral_angle_2_deg 7.485 r_dihedral_angle_1_deg 6.531 r_long_range_B_refined 4.711 r_long_range_B_other 4.384 r_scangle_other 3.069 r_mcangle_it 2.066 r_mcangle_other 2.066 r_scbond_it 1.922 r_scbond_other 1.922 r_angle_refined_deg 1.36 r_mcbond_it 1.296 r_mcbond_other 1.295 r_angle_other_deg 0.478 r_chiral_restr 0.074 r_gen_planes_refined 0.008 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 3488 Nucleic Acid Atoms Solvent Atoms 628 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing Coot model building PDB_EXTRACT data extraction