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Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VXS PDB entry 6VXS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.1 M MES, pH 6.5, 30% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.08 40.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.746 α = 90 b = 33.375 β = 95.086 c = 121.148 γ = 90
Symmetry Space Group P 1 21 1
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 X 6M 2020-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 50 98.6 0.109 0.99 21.3 5.3 52864
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 99.5 1.249 0.54 4.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 6VXS 1.451 40.256 52854 2627 98.264 0.144 0.1421 0.1499 0.1891 0.1973 25.777
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] -0.322 0.737 -0.836 1.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.585 r_dihedral_angle_4_deg 22.141 r_dihedral_angle_3_deg 11.307 r_dihedral_angle_1_deg 6.6 r_scangle_it 5.723 r_scangle_other 5.721 r_rigid_bond_restr 4.39 r_mcangle_it 3.534 r_mcangle_other 3.534 r_mcbond_other 3.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.585 r_dihedral_angle_4_deg 22.141 r_dihedral_angle_3_deg 11.307 r_dihedral_angle_1_deg 6.6 r_scangle_it 5.723 r_scangle_other 5.721 r_rigid_bond_restr 4.39 r_mcangle_it 3.534 r_mcangle_other 3.534 r_mcbond_other 3.079 r_mcbond_it 3.052 r_angle_other_deg 1.689 r_angle_refined_deg 1.683 r_nbd_refined 0.217 r_symmetry_nbd_other 0.192 r_nbd_other 0.18 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.162 r_symmetry_nbd_refined 0.154 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.035 r_bond_other_d 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2535 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing