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SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P80R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 285 22% PEG 3350
200mM Zinc Acetate dihydrate
Crystal Properties Matthews coefficient Solvent content 2.61 52.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.753 α = 90 b = 66.753 β = 90 c = 121.214 γ = 120
Symmetry Space Group P 65 2 2
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 2024-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 121.21 99.9 1 20.2 36.4 13269
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 99.9 0.38 0.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 57.81 13209 692 99.909 0.281 0.277 0.2758 0.3477 0.3484 RANDOM 77.817
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] 1.782 0.891 1.782 -5.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.192 r_dihedral_angle_2_deg 14.176 r_dihedral_angle_3_deg 13.539 r_lrange_other 13.273 r_lrange_it 13.172 r_mcangle_it 10.168 r_mcangle_other 10.162 r_scangle_it 10.108 r_scangle_other 10.101 r_dihedral_angle_1_deg 8.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.192 r_dihedral_angle_2_deg 14.176 r_dihedral_angle_3_deg 13.539 r_lrange_other 13.273 r_lrange_it 13.172 r_mcangle_it 10.168 r_mcangle_other 10.162 r_scangle_it 10.108 r_scangle_other 10.101 r_dihedral_angle_1_deg 8.529 r_scbond_it 7.361 r_mcbond_it 7.327 r_mcbond_other 7.325 r_scbond_other 7.276 r_angle_refined_deg 1.782 r_angle_other_deg 0.721 r_symmetry_nbd_refined 0.321 r_nbd_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.167 r_symmetry_nbd_other 0.156 r_xyhbond_nbd_refined 0.15 r_nbd_other 0.126 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 921 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building BUCCANEER model building Aimless data scaling pointless data scaling STARANISO data scaling autoPROC data reduction XDS data reduction PHASER phasing