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Crystal Structure of SARS-CoV-2 N-CTD in complex with GTP (I)
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 4.6 294 30% PEG 3350
0.1 M sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.773 α = 90 b = 92.719 β = 90.01 c = 68.728 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 PILATUS 6M 2020-11-19 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 1.8 92.72 99.4 0.066 0.071 0.027 0.999 17.8 6.8 50472
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 1.8 1.84 97.8 0.395 0.43 0.169 0.961 6.4
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 1.8 68.73 47930 2511 99.18 0.1581 0.1558 0.1654 0.2033 0.2114 RANDOM 29.782
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] -2.15 0.18 4.25 -2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.248 r_dihedral_angle_4_deg 16.518 r_dihedral_angle_3_deg 15.089 r_dihedral_angle_1_deg 6.49 r_angle_refined_deg 1.937 r_angle_other_deg 1.06 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.248 r_dihedral_angle_4_deg 16.518 r_dihedral_angle_3_deg 15.089 r_dihedral_angle_1_deg 6.49 r_angle_refined_deg 1.937 r_angle_other_deg 1.06 r_chiral_restr 0.125 r_bond_refined_d 0.02 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 3629 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing