☰ Navigation Tabs
Crystal structure of SARS-CoV-2 N-NTD and dsRNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 Malonic Acid, Imidazole, Boric Acid, PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.848 α = 90 b = 39.119 β = 97.605 c = 84.157 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2020-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.18057 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 47.977 99.6 0.049 17.7 4.1 16782
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 0.432
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2OFZ 2.25 47.977 16773 814 99.567 0.228 0.2264 0.2314 0.2685 0.2675 44.328
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] -0.884 -0.434 -2.337 3.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.569 r_dihedral_angle_4_deg 17.179 r_dihedral_angle_3_deg 12.965 r_lrange_it 7.525 r_lrange_other 7.524 r_dihedral_angle_1_deg 6.632 r_paralell_plane_angle_deg 3.194 r_scangle_it 2.833 r_scangle_other 2.833 r_mcangle_it 2.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.569 r_dihedral_angle_4_deg 17.179 r_dihedral_angle_3_deg 12.965 r_lrange_it 7.525 r_lrange_other 7.524 r_dihedral_angle_1_deg 6.632 r_paralell_plane_angle_deg 3.194 r_scangle_it 2.833 r_scangle_other 2.833 r_mcangle_it 2.832 r_mcangle_other 2.831 r_scbond_it 1.731 r_scbond_other 1.731 r_mcbond_it 1.665 r_mcbond_other 1.665 r_angle_refined_deg 1.287 r_angle_other_deg 1.01 r_nbd_other 0.206 r_nbtor_refined 0.184 r_symmetry_nbd_other 0.168 r_nbd_refined 0.159 r_symmetry_nbd_refined 0.157 r_chiral_restr 0.14 r_xyhbond_nbd_refined 0.127 r_symmetry_xyhbond_nbd_refined 0.083 r_symmetry_nbtor_other 0.076 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1815 Nucleic Acid Atoms 590 Solvent Atoms 86 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing