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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 2.78 55.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.8 α = 90 b = 81.76 β = 114.674 c = 51.72 γ = 90
Symmetry Space Group C 1 2 1
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 2023-06-05 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 1.244 47.004 95.4 0.043 0.027 1 12.4 3.4 85942
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 1.244 1.304 0.379 0.258 0.858 2.2
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 1.25 47.004 84289 4118 82.684 0.152 0.1509 0.159 0.1764 0.182 23.515
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] -2.048 0.918 -2.332 2.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.151 r_dihedral_angle_4_deg 15.809 r_dihedral_angle_3_deg 11.952 r_dihedral_angle_1_deg 7.049 r_rigid_bond_restr 6.34 r_lrange_it 4.618 r_lrange_other 4.532 r_scangle_it 4.294 r_scangle_other 4.293 r_scbond_it 3.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.151 r_dihedral_angle_4_deg 15.809 r_dihedral_angle_3_deg 11.952 r_dihedral_angle_1_deg 7.049 r_rigid_bond_restr 6.34 r_lrange_it 4.618 r_lrange_other 4.532 r_scangle_it 4.294 r_scangle_other 4.293 r_scbond_it 3.929 r_scbond_other 3.929 r_mcangle_other 3.096 r_mcangle_it 3.079 r_mcbond_it 2.495 r_mcbond_other 2.413 r_angle_refined_deg 1.815 r_angle_other_deg 1.458 r_nbd_refined 0.225 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.163 r_nbd_other 0.155 r_symmetry_nbd_refined 0.108 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2289 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing