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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2293643386
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 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.208 α = 102.74 b = 70.39 β = 95.87 c = 85.354 γ = 112.42
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 2020-07-29 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 1.97 81.45 96.4 0.086 0.103 0.055 0.998 6.4 3.4 82548
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 1.97 2.01 89 2.12 2.563 1.413 0.263 3.1 4367
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 1.97 81.46 73857 4001 90.97 0.2242 0.2215 0.2352 0.2734 0.2834 RANDOM 53.257
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] 0.87 -0.61 -1.79 -2.44 -0.78 3.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_4_deg 18.257 r_dihedral_angle_3_deg 14.962 r_dihedral_angle_1_deg 7.289 r_mcangle_it 6.64 r_mcbond_other 4.258 r_mcbond_it 4.257 r_angle_refined_deg 1.473 r_angle_other_deg 1.213 r_chiral_restr 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_4_deg 18.257 r_dihedral_angle_3_deg 14.962 r_dihedral_angle_1_deg 7.289 r_mcangle_it 6.64 r_mcbond_other 4.258 r_mcbond_it 4.257 r_angle_refined_deg 1.473 r_angle_other_deg 1.213 r_chiral_restr 0.058 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 454 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing