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SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant D63G
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 8 293 50mM HEPES pH 6.8
150mM Sodium Chloride
24% PEG 3350
2% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.013 α = 90 b = 55.665 β = 95.148 c = 84.895 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 EIGER X 16M 2023-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 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 1.7 84.55 98.9 0.078 0.093 0.049 0.998 12.1 6.6 59866
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 1.7 1.73 1.101 1.303 0.688 0.736 6.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 50.479 58347 2793 96.354 0.232 0.2291 0.2303 0.2802 0.2805 41.319
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] -1.986 -0.312 0.731 1.29
RMS Deviations Key Refinement Restraint Deviation r_scbond_other 42.511 r_scbond_it 42.49 r_scangle_it 38.383 r_scangle_other 38.377 r_lrange_other 34.911 r_mcbond_it 34.72 r_mcbond_other 34.72 r_lrange_it 34.447 r_mcangle_it 27.5 r_mcangle_other 27.495
RMS Deviations Key Refinement Restraint Deviation r_scbond_other 42.511 r_scbond_it 42.49 r_scangle_it 38.383 r_scangle_other 38.377 r_lrange_other 34.911 r_mcbond_it 34.72 r_mcbond_other 34.72 r_lrange_it 34.447 r_mcangle_it 27.5 r_mcangle_other 27.495 r_dihedral_angle_6_deg 13.513 r_dihedral_angle_3_deg 12.57 r_dihedral_angle_2_deg 11.104 r_dihedral_angle_1_deg 7.936 r_angle_refined_deg 2.083 r_angle_other_deg 0.782 r_symmetry_xyhbond_nbd_refined 0.228 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.175 r_symmetry_nbd_other 0.164 r_ncsr_local_group_4 0.138 r_ncsr_local_group_6 0.127 r_ncsr_local_group_2 0.122 r_nbd_other 0.121 r_ncsr_local_group_5 0.115 r_symmetry_nbd_refined 0.112 r_chiral_restr 0.11 r_ncsr_local_group_3 0.103 r_ncsr_local_group_1 0.087 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3794 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement BUSTER refinement Coot model building BUCCANEER model building Aimless data scaling pointless data scaling STARANISO data scaling autoPROC data reduction XDS data reduction PHASER phasing