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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 2.66 53.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.94 α = 90 b = 100.9 β = 90 c = 104.84 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 2023-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 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 1.723 72.7 92.8 0.138 0.057 1 13.4 13.1 55891
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 1.723 1.884 2.1 0.6 0.451 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 FREE R-VALUE 1.723 72.7 55891 2879 72.736 0.212 0.2104 0.2105 0.2383 0.2378 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] -0.001 -0.009 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.603 r_dihedral_angle_6_deg 15.727 r_dihedral_angle_2_deg 10.31 r_lrange_other 8.255 r_lrange_it 8.252 r_dihedral_angle_1_deg 7.577 r_scangle_it 6.395 r_scangle_other 6.394 r_mcangle_other 4.341 r_mcangle_it 4.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.603 r_dihedral_angle_6_deg 15.727 r_dihedral_angle_2_deg 10.31 r_lrange_other 8.255 r_lrange_it 8.252 r_dihedral_angle_1_deg 7.577 r_scangle_it 6.395 r_scangle_other 6.394 r_mcangle_other 4.341 r_mcangle_it 4.34 r_scbond_it 4.14 r_scbond_other 4.139 r_mcbond_it 3.036 r_mcbond_other 3.035 r_angle_refined_deg 1.43 r_angle_other_deg 0.485 r_nbd_refined 0.217 r_symmetry_xyhbond_nbd_refined 0.197 r_symmetry_nbd_refined 0.194 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.183 r_nbd_other 0.164 r_metal_ion_refined 0.162 r_xyhbond_nbd_refined 0.135 r_ncsr_local_group_1 0.114 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_other 0.021 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_dihedral_angle_other_3_deg 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4715 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing