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SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant Q58I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 200mM Ammonium sulfate
10mM Cadmium chloride
25% PEG Smear Medium
100mM HEPES pH 7.5
30mM Manganese chloride
Crystal Properties Matthews coefficient Solvent content 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.78 α = 90 b = 49.715 β = 90 c = 114.248 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2024-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.8929 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.2 114.25 100 0.104 0.106 0.022 0.999 25 43.2 14476
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 0.611 0.629 0.148 0.987 6.4 33.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.2 57.124 14411 718 99.868 0.204 0.2024 0.2058 0.2423 0.2449 49.466
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] 2.053 2.428 -4.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.257 r_dihedral_angle_3_deg 14.567 r_dihedral_angle_2_deg 7.758 r_lrange_it 7.036 r_lrange_other 7.015 r_dihedral_angle_1_deg 5.53 r_scangle_it 5.161 r_scangle_other 5.159 r_scbond_it 4.392 r_scbond_other 4.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.257 r_dihedral_angle_3_deg 14.567 r_dihedral_angle_2_deg 7.758 r_lrange_it 7.036 r_lrange_other 7.015 r_dihedral_angle_1_deg 5.53 r_scangle_it 5.161 r_scangle_other 5.159 r_scbond_it 4.392 r_scbond_other 4.383 r_mcangle_other 3.814 r_mcangle_it 3.812 r_mcbond_it 2.596 r_mcbond_other 2.596 r_angle_refined_deg 1.909 r_angle_other_deg 0.686 r_symmetry_nbd_refined 0.266 r_nbd_other 0.217 r_nbd_refined 0.203 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.022 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_ext_dist_refined_b 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1896 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement BUSTER refinement PDB-REDO refinement Coot model building BUCCANEER model building CRANK2 phasing Aimless data scaling pointless data scaling STARANISO data scaling autoPROC data reduction XDS data reduction