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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z24758179
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 2.35 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.219 α = 102.52 b = 70.236 β = 96.43 c = 85.632 γ = 112.39
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 2020-07-31 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9126 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 2.15 81.51 97.2 0.109 0.131 0.07 0.994 7.5 3.4 64437
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 2.15 2.2 95.3 1.717 2.059 1.118 0.41 3.4 4544
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 6ZSL 2.15 81.63 60959 3333 96.8 0.2115 0.2089 0.2575 0.2302 RANDOM 54.574
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] 0.36 -1.07 -2.44 -2.99 -0.16 4.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.112 r_dihedral_angle_3_deg 16.011 r_dihedral_angle_4_deg 15.998 r_dihedral_angle_1_deg 6.413 r_mcangle_it 5.981 r_mcbond_it 3.766 r_mcbond_other 3.765 r_angle_refined_deg 1.437 r_angle_other_deg 1.244 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.112 r_dihedral_angle_3_deg 16.011 r_dihedral_angle_4_deg 15.998 r_dihedral_angle_1_deg 6.413 r_mcangle_it 5.981 r_mcbond_it 3.766 r_mcbond_other 3.765 r_angle_refined_deg 1.437 r_angle_other_deg 1.244 r_chiral_restr 0.062 r_bond_refined_d 0.006 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 455 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing