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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 Z102768020 (Nprot-x0656)
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 2.94 58.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.486 α = 90 b = 88.486 β = 90 c = 39.378 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 1.678 44.243 54.5 0.06 0.065 0.026 13.1 6.4 9607
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 1.678 1.802 14.1 0.916 1.021 0.441 5.1
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 1.68 62.57 9140 468 54.46 0.20648 0.2026 0.2364 0.27813 0.3141 RANDOM 32.999
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] -0.09 -0.09 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.636 r_dihedral_angle_4_deg 19.205 r_dihedral_angle_3_deg 16.043 r_dihedral_angle_1_deg 7.035 r_long_range_B_refined 5.574 r_long_range_B_other 5.573 r_scangle_other 4.161 r_mcangle_it 3.798 r_mcangle_other 3.796 r_mcbond_other 2.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.636 r_dihedral_angle_4_deg 19.205 r_dihedral_angle_3_deg 16.043 r_dihedral_angle_1_deg 7.035 r_long_range_B_refined 5.574 r_long_range_B_other 5.573 r_scangle_other 4.161 r_mcangle_it 3.798 r_mcangle_other 3.796 r_mcbond_other 2.222 r_mcbond_it 2.201 r_scbond_it 2.008 r_scbond_other 2.007 r_angle_refined_deg 1.436 r_angle_other_deg 1.211 r_chiral_restr 0.058 r_bond_refined_d 0.008 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 127 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction