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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 Z44592329 (Nprot-x0125)
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 2.97 58.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.346 α = 90 b = 88.346 β = 90 c = 39.917 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 2020-08-06 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91259 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 1.754 44.173 44 0.068 0.074 0.029 12.6 6.4 6873
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 1.754 1.887 11.3 0.921 1.026 0.443 5
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 1.75 44.21 6532 341 44.01 0.20371 0.20009 0.2392 0.26892 0.3018 RANDOM 34.443
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 0.06 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.701 r_dihedral_angle_3_deg 17.438 r_dihedral_angle_4_deg 16.197 r_dihedral_angle_1_deg 6.77 r_long_range_B_refined 6.161 r_long_range_B_other 6.159 r_scangle_other 4.029 r_mcangle_it 3.923 r_mcangle_other 3.921 r_scbond_it 2.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.701 r_dihedral_angle_3_deg 17.438 r_dihedral_angle_4_deg 16.197 r_dihedral_angle_1_deg 6.77 r_long_range_B_refined 6.161 r_long_range_B_other 6.159 r_scangle_other 4.029 r_mcangle_it 3.923 r_mcangle_other 3.921 r_scbond_it 2.448 r_scbond_other 2.446 r_mcbond_it 2.361 r_mcbond_other 2.36 r_angle_refined_deg 1.56 r_angle_other_deg 1.203 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 106 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction