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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 2.65 53.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.802 α = 90 b = 101.812 β = 90 c = 103.946 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 2022-10-03 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 1.433 72.735 94.9 0.065 0.027 1 13 6.6 98276
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 1.433 1.543 1.034 0.441 0.584 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 1.433 72.735 98276 4952 74.275 0.162 0.1594 0.1672 0.2168 0.2192 28.676
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] 0.687 -0.793 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.122 r_dihedral_angle_3_deg 14.697 r_dihedral_angle_2_deg 10.718 r_rigid_bond_restr 8.919 r_lrange_it 7.863 r_lrange_other 7.816 r_scangle_it 7.72 r_scangle_other 7.72 r_scbond_it 7.355 r_scbond_other 7.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.122 r_dihedral_angle_3_deg 14.697 r_dihedral_angle_2_deg 10.718 r_rigid_bond_restr 8.919 r_lrange_it 7.863 r_lrange_other 7.816 r_scangle_it 7.72 r_scangle_other 7.72 r_scbond_it 7.355 r_scbond_other 7.353 r_dihedral_angle_1_deg 7.215 r_mcangle_other 6.847 r_mcangle_it 6.846 r_mcbond_it 5.895 r_mcbond_other 5.877 r_angle_refined_deg 1.509 r_angle_other_deg 0.532 r_symmetry_nbd_refined 0.23 r_nbd_refined 0.206 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.154 r_nbd_other 0.153 r_xyhbond_nbd_refined 0.139 r_ncsr_local_group_1 0.117 r_symmetry_xyhbond_nbd_other 0.096 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.075 r_bond_refined_d 0.009 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 4639 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing