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Crystal structure of the C-terminal domain of SARS-CoV-2 nucleocapsid protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2M Ammonium acetate,
0.1M Sodium acetate pH 4.6,
30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.69 54.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.763 α = 106.79 b = 49.458 β = 90.05 c = 68.819 γ = 97.79
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 PILATUS3 S 6M 2020-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 19.82 95.6 0.107 0.065 0.995 5.9 3.5 35328
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 96 0.639 0.391 0.752 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2CJR 2 19.82 33660 1667 95.6 0.191 0.1887 0.2382 0.2393 RANDOM 24.603
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] -2.1 0.27 0.14 3.4 -0.45 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.354 r_dihedral_angle_4_deg 22.69 r_dihedral_angle_3_deg 15.291 r_dihedral_angle_1_deg 7.576 r_angle_refined_deg 1.437 r_angle_other_deg 1.306 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.354 r_dihedral_angle_4_deg 22.69 r_dihedral_angle_3_deg 15.291 r_dihedral_angle_1_deg 7.576 r_angle_refined_deg 1.437 r_angle_other_deg 1.306 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3536 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHENIX phasing