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Crystal structure of SARS-CoV-2 N-CTD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 0.1 M tri-Sodium citrate pH 4.5; 0.1 M bisTris pH 5.5; 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 47.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.843 α = 92.04 b = 44.818 β = 96.2 c = 59.123 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 2020-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.94 58.74 96.2 0.167 0.2 0.109 0.984 6.2 3.4 32080
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.04 96.6 0.844 0.997 0.527 0.704 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 6WZO 1.94 44.79 30433 1635 96.08 0.18 0.1772 0.185 0.233 0.2394 RANDOM 28.385
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] -2.74 -0.12 -0.38 0.66 -0.79 2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.188 r_dihedral_angle_4_deg 18.302 r_dihedral_angle_3_deg 16.11 r_dihedral_angle_1_deg 6.684 r_angle_other_deg 3.669 r_angle_refined_deg 1.828 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_other 0.017 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.188 r_dihedral_angle_4_deg 18.302 r_dihedral_angle_3_deg 16.11 r_dihedral_angle_1_deg 6.684 r_angle_other_deg 3.669 r_angle_refined_deg 1.828 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_other 0.017 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3504 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing