☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with POB0066
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 2.33 47.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.009 α = 103.16 b = 70.028 β = 96.14 c = 85.753 γ = 112.25
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 2020-07-30 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91259 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 2.2 81.54 97.3 0.121 0.145 0.079 0.981 6.7 3.4 59851
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 2.2 2.26 95.3 1.536 1.847 1.007 0.431 3.4 4567
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 2.2 81.56 56711 3098 97.15 0.2158 0.2123 0.2179 0.2805 0.2817 RANDOM 58.912
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] 1.08 -0.24 -2.71 -2.65 -0.69 3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.741 r_dihedral_angle_4_deg 18.864 r_dihedral_angle_3_deg 16.244 r_dihedral_angle_1_deg 7.339 r_mcangle_it 7.266 r_mcbond_other 4.567 r_mcbond_it 4.566 r_angle_refined_deg 1.465 r_angle_other_deg 1.206 r_chiral_restr 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.741 r_dihedral_angle_4_deg 18.864 r_dihedral_angle_3_deg 16.244 r_dihedral_angle_1_deg 7.339 r_mcangle_it 7.266 r_mcbond_other 4.567 r_mcbond_it 4.566 r_angle_refined_deg 1.465 r_angle_other_deg 1.206 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 453 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing