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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 Z2204875953 (Nprot-x0642)
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 3.03 59.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.173 α = 90 b = 88.173 β = 90 c = 40.967 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 2020-08-13 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 1.771 44.087 55.1 0.085 0.093 0.037 7.8 6.4 8538
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 1.771 1.895 15.3 1.081 1.2 0.511 5.2
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 1.77 62.35 8120 419 55.12 0.1994 0.19606 0.236 0.26018 0.2819 RANDOM 30.437
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] -0.24 -0.24 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.334 r_dihedral_angle_3_deg 18.168 r_dihedral_angle_4_deg 16.478 r_dihedral_angle_1_deg 7.141 r_long_range_B_refined 5.46 r_long_range_B_other 5.46 r_mcangle_it 3.205 r_mcangle_other 3.204 r_scangle_other 2.934 r_mcbond_it 2.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.334 r_dihedral_angle_3_deg 18.168 r_dihedral_angle_4_deg 16.478 r_dihedral_angle_1_deg 7.141 r_long_range_B_refined 5.46 r_long_range_B_other 5.46 r_mcangle_it 3.205 r_mcangle_other 3.204 r_scangle_other 2.934 r_mcbond_it 2.015 r_mcbond_other 2.014 r_scbond_it 1.924 r_scbond_other 1.923 r_angle_refined_deg 1.493 r_angle_other_deg 1.261 r_chiral_restr 0.061 r_bond_refined_d 0.008 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 125 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction