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Crystal structure of Ubl1 (residues 18-111) of SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 15% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.73 25.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.53 α = 90 b = 46.333 β = 90 c = 70.077 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2020-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9285 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.93 19.81 99.3 0.094 0.041 0.995 10.7 6 11583
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.98 91.5 0.359 0.222 0.848 2.7 3.2
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 7WZO 1.93 19.81 11544 602 99.116 0.186 0.1841 0.1919 0.2287 0.2356 34.064
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] 0.518 -0.861 0.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.785 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 13.143 r_lrange_other 7.563 r_lrange_it 7.561 r_dihedral_angle_1_deg 6.506 r_scangle_other 5.935 r_scangle_it 5.932 r_scbond_it 4.108 r_scbond_other 4.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.785 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 13.143 r_lrange_other 7.563 r_lrange_it 7.561 r_dihedral_angle_1_deg 6.506 r_scangle_other 5.935 r_scangle_it 5.932 r_scbond_it 4.108 r_scbond_other 4.098 r_mcangle_it 3.885 r_mcangle_other 3.885 r_mcbond_it 2.819 r_mcbond_other 2.796 r_angle_refined_deg 1.536 r_angle_other_deg 1.343 r_symmetry_nbd_refined 0.262 r_symmetry_xyhbond_nbd_refined 0.228 r_nbd_other 0.222 r_xyhbond_nbd_refined 0.211 r_nbd_refined 0.2 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.167 r_ncsr_local_group_1 0.158 r_chiral_restr 0.081 r_symmetry_xyhbond_nbd_other 0.081 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1492 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction Aimless data scaling MOLREP phasing