☰ Navigation Tabs
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 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.76 α = 90 b = 99.54 β = 90 c = 103.52 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 1.00 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 1.788 71.751 92.7 0.224 0.072 1 7.4 10.5 49642
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 1.788 1.94 1.867 0.532 0.542 1.5
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 1.788 71.751 49642 2546 74.19 0.216 0.2142 0.2142 0.2577 0.2577 26.235
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] 0.026 -0.045 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.021 r_dihedral_angle_6_deg 15.782 r_dihedral_angle_2_deg 9.232 r_dihedral_angle_1_deg 7.718 r_lrange_it 7.169 r_lrange_other 7.154 r_scangle_it 5.443 r_scangle_other 5.443 r_mcangle_it 3.997 r_mcangle_other 3.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.021 r_dihedral_angle_6_deg 15.782 r_dihedral_angle_2_deg 9.232 r_dihedral_angle_1_deg 7.718 r_lrange_it 7.169 r_lrange_other 7.154 r_scangle_it 5.443 r_scangle_other 5.443 r_mcangle_it 3.997 r_mcangle_other 3.997 r_scbond_it 3.572 r_scbond_other 3.572 r_mcbond_it 2.723 r_mcbond_other 2.723 r_angle_refined_deg 1.536 r_angle_other_deg 0.524 r_metal_ion_refined 0.259 r_nbd_refined 0.214 r_symmetry_nbd_other 0.197 r_nbd_other 0.197 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.158 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.141 r_dihedral_angle_other_3_deg 0.122 r_ncsr_local_group_1 0.11 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.026 r_gen_planes_refined 0.009 r_bond_refined_d 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 4676 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing