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Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YUN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG4000, 0.2 M Lithium sulfate, 50 mM Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.14 42.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.045 α = 90 b = 43.486 β = 94.45 c = 74.785 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 RIGAKU HyPix-6000HE 2022-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54184
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 1.4 27.46 94.4 0.999 17.2 3.7 85007
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 1.4 1.42 0.832
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6YUN 1.4 24.05 80831 4160 94.27 0.13388 0.13205 0.1419 0.16963 0.1731 RANDOM 10.752
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] 0.42 0.35 -0.9 0.42
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 17.251 r_long_range_B_other 14.282 r_dihedral_angle_3_deg 12.83 r_dihedral_angle_2_deg 10.018 r_scangle_other 6.686 r_dihedral_angle_1_deg 6.556 r_mcangle_other 5.33 r_mcangle_it 5.325 r_scbond_it 4.517 r_scbond_other 4.517
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 17.251 r_long_range_B_other 14.282 r_dihedral_angle_3_deg 12.83 r_dihedral_angle_2_deg 10.018 r_scangle_other 6.686 r_dihedral_angle_1_deg 6.556 r_mcangle_other 5.33 r_mcangle_it 5.325 r_scbond_it 4.517 r_scbond_other 4.517 r_rigid_bond_restr 3.65 r_mcbond_it 3.441 r_mcbond_other 3.424 r_angle_refined_deg 1.963 r_angle_other_deg 0.696 r_chiral_restr 0.106 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3552 Nucleic Acid Atoms Solvent Atoms 831 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing