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Crystal structure of SARS-CoV-2 N-protein C-terminal domain (apo form)
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 37%, 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.
Crystal Properties Matthews coefficient Solvent content 2.19 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.704 α = 90 b = 45.14 β = 93.96 c = 109.061 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 PILATUS 6M KB mirrors, rectangular beam shape 2021-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
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 1.57 48.42 97.4 0.019 0.999 21.2 6.4 123141 19.806
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 1.57 1.6 74.1 0.531 0.647 1.2 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 1.57 48.42 116789 6337 97.39 0.19093 0.18887 0.1996 0.22854 0.2356 RANDOM 23.748
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] 0.3 -0.32 0.73 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.708 r_dihedral_angle_1_deg 6.549 r_long_range_B_refined 6.292 r_long_range_B_other 6.13 r_dihedral_angle_2_deg 5.822 r_scangle_other 4.658 r_scbond_it 3.042 r_scbond_other 3.042 r_mcangle_it 2.937 r_mcangle_other 2.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.708 r_dihedral_angle_1_deg 6.549 r_long_range_B_refined 6.292 r_long_range_B_other 6.13 r_dihedral_angle_2_deg 5.822 r_scangle_other 4.658 r_scbond_it 3.042 r_scbond_other 3.042 r_mcangle_it 2.937 r_mcangle_other 2.937 r_mcbond_it 2.041 r_mcbond_other 2.041 r_angle_refined_deg 1.531 r_angle_other_deg 0.51 r_chiral_restr 0.077 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 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 1041 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing BUCCANEER model building Coot model building PDB_EXTRACT data extraction