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SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WRH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 289 0.2 M ammonium iodide, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.173 α = 90 b = 113.693 β = 93.02 c = 109.688 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 2021-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 1.32 49.39 99.3 0.136 0.141 0.035 0.985 6.3 12.9 169862
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 1.32 1.35 92.1 1.39 1.522 0.597 0.513 1.13 5.3
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 6wrh 1.32 49.39 161093 8728 98.59 0.147 0.1446 0.1445 0.1909 0.1912 RANDOM 23.621
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] 0.39 0.17 0.53 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.867 r_dihedral_angle_4_deg 22.303 r_dihedral_angle_3_deg 12.343 r_dihedral_angle_1_deg 6.467 r_rigid_bond_restr 2.561 r_angle_refined_deg 1.45 r_angle_other_deg 1.422 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.867 r_dihedral_angle_4_deg 22.303 r_dihedral_angle_3_deg 12.343 r_dihedral_angle_1_deg 6.467 r_rigid_bond_restr 2.561 r_angle_refined_deg 1.45 r_angle_other_deg 1.422 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6255 Nucleic Acid Atoms Solvent Atoms 880 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing