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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 53.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.05 α = 90 b = 100.75 β = 90 c = 104.53 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 2023-06-02 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 1.709 72.541 95.2 0.105 0.03 1 16.8 13.2 59132
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 1.709 1.861 70.8 1.587 0.495 0.587 1.7
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 1.709 72.541 59132 2970 75.363 0.204 0.2024 0.2024 0.2419 0.2424 28.662
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 -0.017 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.485 r_dihedral_angle_6_deg 15.792 r_dihedral_angle_2_deg 8.47 r_dihedral_angle_1_deg 7.424 r_lrange_it 7.051 r_lrange_other 7.037 r_scangle_it 5.373 r_scangle_other 5.372 r_mcangle_other 3.939 r_mcangle_it 3.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.485 r_dihedral_angle_6_deg 15.792 r_dihedral_angle_2_deg 8.47 r_dihedral_angle_1_deg 7.424 r_lrange_it 7.051 r_lrange_other 7.037 r_scangle_it 5.373 r_scangle_other 5.372 r_mcangle_other 3.939 r_mcangle_it 3.938 r_scbond_it 3.616 r_scbond_other 3.615 r_mcbond_it 2.715 r_mcbond_other 2.71 r_angle_refined_deg 1.483 r_angle_other_deg 0.512 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.179 r_metal_ion_refined 0.16 r_nbd_other 0.155 r_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.137 r_ncsr_local_group_1 0.117 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.076 r_bond_refined_d 0.008 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 4701 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing