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PanDDA analysis group deposition of ground-state model of SARS-CoV-2 helicase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZSL 6ZSL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 16 % Ethylene Glycol, 8 % PEG 8K, 0.05 M HEPES, 0.05 M MOPS, 0.03 M Sodium Nitrate, 0,03 M Sodium Phosphate, 0.03 M Ammonium Sulphate
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.242 α = 102.4 b = 70.282 β = 95.71 c = 84.616 γ = 112.84
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 2020-07-16 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91256 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.87 80.92 96 8.2 95763
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 6ZSL 1.87 80.92 89656 4861 94.71 0.2205 0.2187 0.225 0.2538 0.2577 RANDOM 42.322
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] 0.14 -0.51 -0.95 -1.24 -0.03 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.011 r_dihedral_angle_4_deg 17.466 r_dihedral_angle_3_deg 14.105 r_dihedral_angle_1_deg 7.142 r_mcangle_it 5.02 r_mcbond_it 3.407 r_mcbond_other 3.404 r_angle_refined_deg 1.491 r_angle_other_deg 1.287 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.011 r_dihedral_angle_4_deg 17.466 r_dihedral_angle_3_deg 14.105 r_dihedral_angle_1_deg 7.142 r_mcangle_it 5.02 r_mcbond_it 3.407 r_mcbond_other 3.404 r_angle_refined_deg 1.491 r_angle_other_deg 1.287 r_chiral_restr 0.066 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 8917 Nucleic Acid Atoms Solvent Atoms 456 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing