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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1354370680
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 2.66 53.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.596 α = 90 b = 67.536 β = 90 c = 138.752 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 2022-02-03 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) 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 2.21 138.76 99.9 0.274 0.297 0.113 0.988 5.2 6.7 32615
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 2.21 2.28 98.8 3.555 3.84 1.44 0.292 7 2774
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 2.21 69.38 30804 1533 99.19 0.2235 0.2203 0.2288 0.2846 0.2916 RANDOM 56.434
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] -1.49 5.58 -4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.106 r_dihedral_angle_4_deg 17.172 r_dihedral_angle_3_deg 16.969 r_dihedral_angle_1_deg 8.245 r_mcangle_it 7.345 r_mcbond_it 4.632 r_mcbond_other 4.631 r_angle_refined_deg 1.448 r_angle_other_deg 1.233 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.106 r_dihedral_angle_4_deg 17.172 r_dihedral_angle_3_deg 16.969 r_dihedral_angle_1_deg 8.245 r_mcangle_it 7.345 r_mcbond_it 4.632 r_mcbond_other 4.631 r_angle_refined_deg 1.448 r_angle_other_deg 1.233 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 427 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing