☰ Navigation Tabs
Crystal Structure of ADP ribose phosphatase of NSP3 from SARS-CoV-2 in the apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 289 34.3% PEG 5000 MME, 150 mM AMPD/Tris, pH 9.0, 30 mM K/NA tartrate
Crystal Properties Matthews coefficient Solvent content 2.11 41.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.671 α = 90 b = 29.677 β = 103.52 c = 37.886 γ = 90
Symmetry Space Group C 1 2 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 mirrors 2020-03-31 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 1.35 50 95.7 0.089 0.994 24.13 6.2 32168 -3
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 1.35 1.37 91.4 0.483 0.747 2.65 2.7
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 MOLECULAR REPLACEMENT THROUGHOUT 6WCF 1.35 36.86 30573 1595 95.63 0.1057 0.1036 0.104 0.1441 0.1436 RANDOM 13.639
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] 0.75 0.67 -0.19 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.408 r_dihedral_angle_4_deg 26.327 r_dihedral_angle_3_deg 9.359 r_dihedral_angle_1_deg 6.509 r_rigid_bond_restr 1.984 r_angle_refined_deg 1.659 r_angle_other_deg 1.592 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.408 r_dihedral_angle_4_deg 26.327 r_dihedral_angle_3_deg 9.359 r_dihedral_angle_1_deg 6.509 r_rigid_bond_restr 1.984 r_angle_refined_deg 1.659 r_angle_other_deg 1.592 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1273 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing