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Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ampicillin
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, Ampicillin
Crystal Properties Matthews coefficient Solvent content 1.64 25.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.582 α = 90 b = 43.604 β = 108.66 c = 56.762 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 2023-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.2 24.17 99.8 0.993 29.4 5.5 10644
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 2.27 0.981
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 2.2 24.17 10145 486 99.61 0.18225 0.17964 0.1944 0.23827 0.2494 RANDOM 13.223
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] 0.06 0.11 -0.18 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.98 r_dihedral_angle_3_deg 16.355 r_dihedral_angle_1_deg 7.538 r_long_range_B_refined 5.116 r_long_range_B_other 4.894 r_scangle_other 2.381 r_angle_refined_deg 1.562 r_mcangle_it 1.486 r_mcangle_other 1.485 r_scbond_it 1.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.98 r_dihedral_angle_3_deg 16.355 r_dihedral_angle_1_deg 7.538 r_long_range_B_refined 5.116 r_long_range_B_other 4.894 r_scangle_other 2.381 r_angle_refined_deg 1.562 r_mcangle_it 1.486 r_mcangle_other 1.485 r_scbond_it 1.435 r_scbond_other 1.435 r_mcbond_it 0.868 r_mcbond_other 0.858 r_angle_other_deg 0.505 r_chiral_restr 0.075 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 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 1727 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing