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2.05 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CJR PDB entry 2CJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 20.0 mg/mL protein in 0.1 M sodium chloride, 0.01 M Tris, pH 8.3 against Classics II screen D8 (0.1 M HEPES, pH 7.5, 25% w/v PEG3350)
Crystal Properties Matthews coefficient Solvent content 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.612 α = 90 b = 122.317 β = 90 c = 130.633 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 CCD MARMOSAIC 300 mm CCD Be 2020-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.05 30 97 0.171 0.171 0.187 0.073 0.976 9.7 6.2 43336 -3 17.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 80.6 0.63 0.63 0.697 0.288 0.698 2.6 5.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 2CJR 2.052 29.881 43303 2192 96.857 0.189 0.1869 0.1928 0.2275 0.2323 18.645
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] 1.169 -0.386 -0.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.429 r_dihedral_angle_4_deg 9.126 r_dihedral_angle_3_deg 7.608 r_lrange_it 4.641 r_lrange_other 4.398 r_dihedral_angle_1_deg 2.439 r_scangle_it 1.621 r_scangle_other 1.621 r_angle_refined_deg 1.493 r_mcangle_it 1.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.429 r_dihedral_angle_4_deg 9.126 r_dihedral_angle_3_deg 7.608 r_lrange_it 4.641 r_lrange_other 4.398 r_dihedral_angle_1_deg 2.439 r_scangle_it 1.621 r_scangle_other 1.621 r_angle_refined_deg 1.493 r_mcangle_it 1.322 r_mcangle_other 1.322 r_scbond_it 0.96 r_scbond_other 0.96 r_mcbond_it 0.769 r_mcbond_other 0.769 r_angle_other_deg 0.394 r_nbd_refined 0.208 r_nbd_other 0.191 r_symmetry_nbd_refined 0.187 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.095 r_chiral_restr 0.072 r_gen_planes_refined 0.053 r_gen_planes_other 0.048 r_bond_refined_d 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5196 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing