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Crystal structure of SARS-CoV-2 (Covid-19) Nsp3 macrodomain in complex with NDPr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM Tris-HCl, pH 8, 200 mM sodium acetate, 30% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.19 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.496 α = 79.153 b = 47.084 β = 72.053 c = 65.726 γ = 74.297
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 EIGER2 S 16M 2023-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE 7B2 0.96860 CHESS 7B2
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 1.395 29.06 94.33 0.05423 0.06424 0.03404 0.998 12.18 3.5 93149 18.03
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 1.395 1.43 78.78 0.6008 0.7468 0.4341 0.728 1.38 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 6YWL 1.395 29.06 1.97 93135 2000 94.33 0.153 0.1523 0.166 0.1844 0.1905 27.87
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.535 f_angle_d 1.0925 f_chiral_restr 0.0766 f_bond_d 0.0101 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3804 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 114
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building