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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z198195770
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 53.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.606 α = 90 b = 67.764 β = 90 c = 138.339 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 2.01 138.37 99.9 0.236 0.256 0.097 0.99 6.6 6.8 43194
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 2.01 2.06 98.3 2.851 3.081 1.157 0.358 7 3094
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 7QGI 2.01 69.17 40957 2068 99.65 0.2038 0.2017 0.2451 0.2145 RANDOM 41.983
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] -1.31 4.33 -3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.763 r_dihedral_angle_4_deg 17.342 r_dihedral_angle_3_deg 15.963 r_dihedral_angle_1_deg 8.402 r_mcangle_it 6.142 r_mcbond_it 3.999 r_mcbond_other 3.978 r_angle_refined_deg 1.589 r_angle_other_deg 1.321 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.763 r_dihedral_angle_4_deg 17.342 r_dihedral_angle_3_deg 15.963 r_dihedral_angle_1_deg 8.402 r_mcangle_it 6.142 r_mcbond_it 3.999 r_mcbond_other 3.978 r_angle_refined_deg 1.589 r_angle_other_deg 1.321 r_chiral_restr 0.074 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 3679 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing