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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 Z1407672867 (Nprot-x0389)
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 = 88.195 α = 90 b = 88.195 β = 90 c = 41.165 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 1.627 37.302 52.1 0.079 0.086 0.034 10.3 6.3 10435
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 1.627 1.751 13.3 0.871 0.98 0.438 4.6
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 1.63 62.36 9913 523 52.03 0.19523 0.19198 0.233 0.25528 0.2834 RANDOM 29.162
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] -0.04 -0.04 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.21 r_dihedral_angle_4_deg 17.788 r_dihedral_angle_3_deg 16.732 r_dihedral_angle_1_deg 7.351 r_long_range_B_refined 6.431 r_long_range_B_other 6.43 r_scangle_other 3.063 r_mcangle_it 2.951 r_mcangle_other 2.95 r_mcbond_it 1.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.21 r_dihedral_angle_4_deg 17.788 r_dihedral_angle_3_deg 16.732 r_dihedral_angle_1_deg 7.351 r_long_range_B_refined 6.431 r_long_range_B_other 6.43 r_scangle_other 3.063 r_mcangle_it 2.951 r_mcangle_other 2.95 r_mcbond_it 1.918 r_mcbond_other 1.896 r_scbond_it 1.884 r_scbond_other 1.883 r_angle_refined_deg 1.434 r_angle_other_deg 1.246 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 162 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction