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SARS-CoV-2 Nucleocapsid N-terminal domain NTD
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 20% PEG 6000
100mM MES pH 6.0
10mM Zinc Chloride
Crystal Properties Matthews coefficient Solvent content 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.916 α = 90 b = 93.073 β = 90 c = 96.936 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 2022-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 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 2.3 96.98 99.7 0.203 0.212 0.062 0.998 11.8 21 24362 1.02
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 2.3 2.38 100 4.069 4.252 1.224 0.599 0.9 22
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 2.3 67.14 24288 1154 99.7 0.271 0.2686 0.2529 0.32 0.2948 RANDOM 63.61
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] 19.9827 -5.2236 -14.7591
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.12 t_omega_torsion 2.76 t_angle_deg 0.9 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3913 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms
Software Software Software Name Purpose 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