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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z85956652
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 47.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.94 α = 102.81 b = 70.101 β = 95.84 c = 85.447 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 2020-07-30 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 2.42 81.47 97.2 0.121 0.144 0.077 0.969 6.3 3.4 44396
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 2.42 2.52 95.4 1.383 1.653 0.89 0.335 3.4 4584
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 2.43 81.52 42006 2298 97 0.2112 0.207 0.2197 0.2885 0.2923 RANDOM 59.33
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] 0.88 -0.48 -2.47 -1.37 -1 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.091 r_dihedral_angle_4_deg 17.44 r_dihedral_angle_3_deg 15.691 r_mcangle_it 8.828 r_dihedral_angle_1_deg 7.777 r_mcbond_it 5.81 r_mcbond_other 5.808 r_angle_refined_deg 1.611 r_angle_other_deg 1.235 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.091 r_dihedral_angle_4_deg 17.44 r_dihedral_angle_3_deg 15.691 r_mcangle_it 8.828 r_dihedral_angle_1_deg 7.777 r_mcbond_it 5.81 r_mcbond_other 5.808 r_angle_refined_deg 1.611 r_angle_other_deg 1.235 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8917 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing