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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 2.64 53.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.76 α = 90 b = 100.96 β = 90 c = 104.31 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) 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 1.309 104.3 92.8 0.082 1 12.7 6.8 134158
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.309 1.428 1.101 0.657 1.9
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 1.309 72.545 134091 6631 77.967 0.147 0.1457 0.1542 0.18 0.1844 18.513
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] 2.851 -1.424 -1.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.295 r_dihedral_angle_4_deg 17.958 r_dihedral_angle_3_deg 11.772 r_rigid_bond_restr 8.918 r_dihedral_angle_1_deg 7.263 r_lrange_it 5 r_lrange_other 4.878 r_scangle_it 4.58 r_scangle_other 4.579 r_scbond_it 3.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.295 r_dihedral_angle_4_deg 17.958 r_dihedral_angle_3_deg 11.772 r_rigid_bond_restr 8.918 r_dihedral_angle_1_deg 7.263 r_lrange_it 5 r_lrange_other 4.878 r_scangle_it 4.58 r_scangle_other 4.579 r_scbond_it 3.883 r_scbond_other 3.882 r_mcangle_other 3.686 r_mcangle_it 3.685 r_mcbond_it 2.973 r_mcbond_other 2.962 r_angle_refined_deg 2.004 r_angle_other_deg 1.601 r_symmetry_nbd_refined 0.273 r_symmetry_xyhbond_nbd_refined 0.268 r_nbd_refined 0.226 r_nbd_other 0.205 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.144 r_ncsr_local_group_1 0.135 r_chiral_restr 0.114 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4697 Nucleic Acid Atoms Solvent Atoms 591 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing