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Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2, crystal form II
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 EVAPORATION 277 tba
Crystal Properties Matthews coefficient Solvent content 2.75 55.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.203 α = 90 b = 88.203 β = 90 c = 42.763 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 PILATUS 6M 2020-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.36 44.096 97.8 0.041 0.047 0.016 20.2 7.6 34588
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.361 1.43 86.6 1.093 1.093 1.446 0.698 0.7 3.5
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 1.361 30 32473 1709 96.81 0.1517 0.1495 0.1627 0.1962 0.2111 RANDOM 28.894
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] -1.14 -1.14 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.809 r_sphericity_free 26.737 r_dihedral_angle_4_deg 17.93 r_dihedral_angle_3_deg 13.639 r_sphericity_bonded 12.693 r_dihedral_angle_1_deg 6.069 r_rigid_bond_restr 3.06 r_angle_refined_deg 1.645 r_angle_other_deg 1.023 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.809 r_sphericity_free 26.737 r_dihedral_angle_4_deg 17.93 r_dihedral_angle_3_deg 13.639 r_sphericity_bonded 12.693 r_dihedral_angle_1_deg 6.069 r_rigid_bond_restr 3.06 r_angle_refined_deg 1.645 r_angle_other_deg 1.023 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 936 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction PHENIX phasing