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Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone
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 2.67 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.539 α = 106.66 b = 46.643 β = 90.11 c = 69.021 γ = 93.46
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 2022-08-24 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 2 26.58 99.2 0.997 17.8 4.2 34801
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 2 2.05 0.889 3.8
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 2 26.58 33047 1752 99.18 0.15019 0.14731 0.1599 0.20494 0.2123 RANDOM 16.983
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] -1.28 -0.03 -0.12 1.07 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.586 r_dihedral_angle_3_deg 14.035 r_dihedral_angle_1_deg 7.341 r_long_range_B_refined 6.47 r_long_range_B_other 6.47 r_scangle_other 3.835 r_scbond_it 2.365 r_scbond_other 2.365 r_mcangle_it 2.086 r_mcangle_other 2.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.586 r_dihedral_angle_3_deg 14.035 r_dihedral_angle_1_deg 7.341 r_long_range_B_refined 6.47 r_long_range_B_other 6.47 r_scangle_other 3.835 r_scbond_it 2.365 r_scbond_other 2.365 r_mcangle_it 2.086 r_mcangle_other 2.086 r_angle_refined_deg 1.844 r_mcbond_it 1.295 r_mcbond_other 1.29 r_angle_other_deg 0.662 r_chiral_restr 0.551 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3548 Nucleic Acid Atoms Solvent Atoms 669 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction Aimless data scaling MOLREP phasing