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Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z744754722 (Nprot-x0467)
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 7.8 298 0.1 M HEPES, pH 7.8, 10 % isopropanol, 23 % PEG4000
Crystal Properties Matthews coefficient Solvent content 3.05 59.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.505 α = 90 b = 88.505 β = 90 c = 40.877 γ = 90
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 EIGER2 XE 9M 2020-08-12 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91261 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.658 62.582 52.7 0.058 0.063 0.025 14.3 6.3 9988
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.658 1.796 12.7 0.802 0.894 0.384 4.9
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 1.66 62.58 9486 502 52.7 0.20286 0.19893 0.237 0.27561 0.2933 RANDOM 29.42
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] 0.03 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.645 r_dihedral_angle_3_deg 17.296 r_dihedral_angle_4_deg 17.193 r_dihedral_angle_1_deg 6.783 r_long_range_B_refined 5.993 r_long_range_B_other 5.991 r_mcangle_it 3.109 r_mcangle_other 3.109 r_scangle_other 3.088 r_mcbond_it 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.645 r_dihedral_angle_3_deg 17.296 r_dihedral_angle_4_deg 17.193 r_dihedral_angle_1_deg 6.783 r_long_range_B_refined 5.993 r_long_range_B_other 5.991 r_mcangle_it 3.109 r_mcangle_other 3.109 r_scangle_other 3.088 r_mcbond_it 1.98 r_mcbond_other 1.979 r_scbond_it 1.945 r_scbond_other 1.943 r_angle_refined_deg 1.446 r_angle_other_deg 1.225 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 918 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction