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Crystal Structure of SARS-CoV-2 N-CTD in complex with GTP (II)
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 and 0.1 M sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.25 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.691 α = 74.37 b = 48.408 β = 89.89 c = 68.668 γ = 83.17
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 2 66.09 95.5 0.082 0.098 0.052 0.993 8.9 3.4 34712
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 2 2.05 93.2 0.315 0.382 0.212 0.923 3.1
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 2 66.09 32981 1730 95.45 0.1924 0.1898 0.1973 0.2406 0.2435 RANDOM 33.999
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] -2.76 0.09 -0.49 5.82 -0.06 -2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.759 r_dihedral_angle_3_deg 15.983 r_dihedral_angle_4_deg 15.976 r_dihedral_angle_1_deg 7.183 r_angle_refined_deg 1.783 r_angle_other_deg 0.998 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.759 r_dihedral_angle_3_deg 15.983 r_dihedral_angle_4_deg 15.976 r_dihedral_angle_1_deg 7.183 r_angle_refined_deg 1.783 r_angle_other_deg 0.998 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3541 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing