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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 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.12 α = 90 b = 100.11 β = 90 c = 104.31 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 2022-06-29 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 1.705 72.228 93.8 0.133 0.038 1 13.6 13.2 60607
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 1.705 1.866 51.1 1.987 0.57 0.458 1.8
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 1.705 72.228 60607 3114 77.24 0.199 0.1973 0.1974 0.2293 0.2293 30.608
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] 0.014 -0.058 0.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.381 r_dihedral_angle_6_deg 16.228 r_dihedral_angle_2_deg 9.808 r_lrange_it 8.46 r_lrange_other 8.457 r_dihedral_angle_1_deg 7.431 r_scangle_it 6.617 r_scangle_other 6.576 r_scbond_it 4.38 r_scbond_other 4.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.381 r_dihedral_angle_6_deg 16.228 r_dihedral_angle_2_deg 9.808 r_lrange_it 8.46 r_lrange_other 8.457 r_dihedral_angle_1_deg 7.431 r_scangle_it 6.617 r_scangle_other 6.576 r_scbond_it 4.38 r_scbond_other 4.343 r_mcangle_it 3.976 r_mcangle_other 3.976 r_mcbond_it 2.857 r_mcbond_other 2.854 r_angle_refined_deg 1.529 r_angle_other_deg 0.511 r_symmetry_nbd_refined 0.303 r_symmetry_xyhbond_nbd_refined 0.234 r_nbd_refined 0.224 r_nbd_other 0.213 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.181 r_metal_ion_refined 0.164 r_xyhbond_nbd_refined 0.142 r_ncsr_local_group_1 0.112 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.013 r_gen_planes_refined 0.008 r_bond_refined_d 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 4676 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing