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PanDDA analysis group deposition of ground-state model of SARS-CoV-2 NSP14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QGI 7QGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 278 1.26 M sodium phosphate monobasic, 0.14 M potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 2.67 53.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.538 α = 90 b = 68.093 β = 90 c = 138.425 γ = 90
Symmetry Space Group P 21 21 21
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 2021-12-10 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91788 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.655 69.213 91.5 0.139 0.059 0.997 9.1 5.5 39137
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.655 1.851 65.4 1.17 0.466 0.713 6.2 1958
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 FOURIER SYNTHESIS THROUGHOUT 7QGI 1.65 69.31 37240 1897 50.92 0.1919 0.1906 0.1968 0.2173 0.2212 RANDOM 25.292
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] -0.13 0.54 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.719 r_dihedral_angle_4_deg 15.036 r_dihedral_angle_3_deg 14.359 r_dihedral_angle_1_deg 7.527 r_mcangle_it 4.832 r_mcbond_it 2.864 r_mcbond_other 2.863 r_angle_refined_deg 1.481 r_angle_other_deg 1.33 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.719 r_dihedral_angle_4_deg 15.036 r_dihedral_angle_3_deg 14.359 r_dihedral_angle_1_deg 7.527 r_mcangle_it 4.832 r_mcbond_it 2.864 r_mcbond_other 2.863 r_angle_refined_deg 1.481 r_angle_other_deg 1.33 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3666 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing