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Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 5 (P43 crystal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 100 mM CHES pH 9.5, 28% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.14 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.393 α = 90 b = 88.393 β = 90 c = 39.924 γ = 90
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 PILATUS3 S 6M 2021-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.7749 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 0.9 44.2 99.88 0.02331 40.56 6.6 227204 6.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.9 0.9327 0.1446
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 7QKO 0.9 44.2 1.36 227197 11026 99.89 0.0955 0.095 0.095 0.1066 0.1064 11.7
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 15.2156 f_angle_d 1.2504 f_chiral_restr 0.0851 f_bond_d 0.0107 f_plane_restr 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2542 Nucleic Acid Atoms Solvent Atoms 698 Heterogen Atoms 62
Software Software Software Name Purpose XDS data reduction PHENIX refinement XDS data scaling PHASER phasing Coot model building