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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 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.93 α = 90 b = 99.19 β = 90 c = 103.68 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 1.73 56.89 93.6 0.178 0.051 1 9.7 13.3 51632
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 1.73 1.926 1.76 0.493 0.623 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 1.73 56.885 51632 2655 69.958 0.217 0.2154 0.2153 0.2569 0.2569 27.621
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] 0.012 -0.034 0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.172 r_dihedral_angle_6_deg 15.758 r_dihedral_angle_2_deg 8.342 r_dihedral_angle_1_deg 7.493 r_lrange_it 7.214 r_lrange_other 7.197 r_scangle_it 5.182 r_scangle_other 5.159 r_mcangle_other 3.578 r_mcangle_it 3.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.172 r_dihedral_angle_6_deg 15.758 r_dihedral_angle_2_deg 8.342 r_dihedral_angle_1_deg 7.493 r_lrange_it 7.214 r_lrange_other 7.197 r_scangle_it 5.182 r_scangle_other 5.159 r_mcangle_other 3.578 r_mcangle_it 3.577 r_scbond_it 3.338 r_scbond_other 3.307 r_mcbond_it 2.355 r_mcbond_other 2.352 r_angle_refined_deg 1.45 r_angle_other_deg 0.484 r_symmetry_xyhbond_nbd_refined 0.293 r_nbd_refined 0.23 r_nbd_other 0.2 r_symmetry_nbd_other 0.196 r_metal_ion_refined 0.181 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.152 r_ncsr_local_group_1 0.111 r_symmetry_nbtor_other 0.083 r_xyhbond_nbd_other 0.073 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.007 r_gen_planes_refined 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 4697 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing