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Crystal Structure of L516C/Y647C Mutant of SARS-Unique Domain (SUD) from SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 292 Protein: 6.45 mg/ml, 0.3M Sodium chloride, 0.01M Tris pH 8.3; Screen: AmSO4 (A2), 0.2M Ammonium acetate, 2.2M Ammonium sulfate; Cryo: 2.0M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.274 α = 90 b = 86.274 β = 90 c = 76.674 γ = 120
Symmetry Space Group P 31 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 EIGER X 9M 2021-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12704 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.65 30 99.9 0.1 0.1 0.102 0.024 1 30.1 18.8 40007 -3 26.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 99.7 0.437 0.772 2 14.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.65 28.26 37981 1997 99.81 0.186 0.1848 0.2079 0.2452 RANDOM 37.172
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] 1.61 0.8 1.61 -5.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.193 r_dihedral_angle_4_deg 13.442 r_dihedral_angle_3_deg 8.384 r_dihedral_angle_1_deg 4.168 r_angle_refined_deg 1.454 r_angle_other_deg 0.343 r_chiral_restr 0.058 r_gen_planes_refined 0.055 r_gen_planes_other 0.051 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.193 r_dihedral_angle_4_deg 13.442 r_dihedral_angle_3_deg 8.384 r_dihedral_angle_1_deg 4.168 r_angle_refined_deg 1.454 r_angle_other_deg 0.343 r_chiral_restr 0.058 r_gen_planes_refined 0.055 r_gen_planes_other 0.051 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1921 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing