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Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 9 (P43 crystal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KQO
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 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.585 α = 90 b = 88.585 β = 90 c = 39.664 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 0.7748 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 39.62 99.89 0.02697 28.95 6.5 226515 8.32
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 0.933 0.4164
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 7KQO 0.9 39.62 1.34 226508 11000 99.89 0.1103 0.1096 0.1101 0.1258 0.1259 14.7
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 13.2478 f_angle_d 1.099 f_chiral_restr 0.0792 f_plane_restr 0.0127 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2550 Nucleic Acid Atoms Solvent Atoms 763 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction PHENIX refinement PHASER phasing XDS data scaling Coot model building