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SARS-CoV-2 with a bound inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in-house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
Crystal Properties Matthews coefficient Solvent content 2.64 53.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.91 α = 90 b = 100.79 β = 90 c = 104.49 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 EIGER X 16M 2022-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
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 1.893 72.542 91.4 0.114 0.033 1 15.1 12.6 37130
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 1.893 2.108 1.279 0.461 0.564 1.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.893 72.542 37130 1926 64.217 0.236 0.2341 0.2344 0.2713 0.2707 34.199
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] 0.018 0.002 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.39 r_dihedral_angle_6_deg 15.518 r_dihedral_angle_1_deg 8 r_lrange_it 7.601 r_lrange_other 7.6 r_dihedral_angle_2_deg 7.371 r_scangle_it 5.789 r_scangle_other 5.788 r_mcangle_it 4.63 r_mcangle_other 4.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.39 r_dihedral_angle_6_deg 15.518 r_dihedral_angle_1_deg 8 r_lrange_it 7.601 r_lrange_other 7.6 r_dihedral_angle_2_deg 7.371 r_scangle_it 5.789 r_scangle_other 5.788 r_mcangle_it 4.63 r_mcangle_other 4.63 r_scbond_it 3.836 r_scbond_other 3.828 r_mcbond_it 3.132 r_mcbond_other 3.115 r_angle_refined_deg 1.508 r_angle_other_deg 0.499 r_nbd_refined 0.225 r_nbd_other 0.198 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.173 r_symmetry_nbd_refined 0.159 r_xyhbond_nbd_refined 0.131 r_ncsr_local_group_1 0.12 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.048 r_bond_refined_d 0.008 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 4662 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing