☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z57614330
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 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.479 α = 102.71 b = 70.417 β = 95.94 c = 85.584 γ = 112.61
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 1.92 81.64 95.8 0.075 0.09 0.048 0.997 7.4 3.4 89117
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 1.92 1.96 89.2 1.365 1.675 0.951 0.474 3 4247
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 1.92 81.65 83487 4488 94.64 0.2196 0.2174 0.2305 0.2605 0.2717 RANDOM 46.172
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] 0.71 -0.69 -1.42 -1.98 -0.02 2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.659 r_dihedral_angle_4_deg 19.252 r_dihedral_angle_3_deg 15.2 r_dihedral_angle_1_deg 6.735 r_mcangle_it 6.131 r_mcbond_it 4.05 r_mcbond_other 4.048 r_angle_refined_deg 1.55 r_angle_other_deg 1.27 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.659 r_dihedral_angle_4_deg 19.252 r_dihedral_angle_3_deg 15.2 r_dihedral_angle_1_deg 6.735 r_mcangle_it 6.131 r_mcbond_it 4.05 r_mcbond_other 4.048 r_angle_refined_deg 1.55 r_angle_other_deg 1.27 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 58
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing