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PanDDA analysis group deposition of ground-state model of SARS-CoV-2 NendoU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X1B 6X1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 0.1 M Na3 Citrate pH 5,14% w/v PEG6000
Crystal Properties Matthews coefficient Solvent content 4.62 73.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.997 α = 90 b = 149.997 β = 90 c = 111.405 γ = 120
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 2M 2020-01-10 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9127 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.64 130.31 99.9 0.09 1 12.2 1560712
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.67 98.7 2.458 0.33 8585
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 6X1B 1.64 129.98 161483 8654 97.8 0.1887 0.1875 0.1982 0.2111 0.2196 RANDOM 32.016
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] -0.74 -0.37 -0.74 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_3_deg 13.715 r_dihedral_angle_4_deg 12.607 r_dihedral_angle_1_deg 7.173 r_mcangle_it 3.986 r_mcbond_it 2.886 r_mcbond_other 2.885 r_angle_refined_deg 1.767 r_angle_other_deg 1.5 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_3_deg 13.715 r_dihedral_angle_4_deg 12.607 r_dihedral_angle_1_deg 7.173 r_mcangle_it 3.986 r_mcbond_it 2.886 r_mcbond_other 2.885 r_angle_refined_deg 1.767 r_angle_other_deg 1.5 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5498 Nucleic Acid Atoms Solvent Atoms 966 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing