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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 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.9 α = 90 b = 99.2 β = 90 c = 103.38 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 1.781 71.6 95.1 0.198 0.056 1 11.9 13.4 55779
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 1.781 1.919 1.965 0.552 0.504 1.6
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 1.781 71.577 55779 2853 82.659 0.22 0.2185 0.2186 0.2501 0.25 32.268
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] -0.099 0.28 -0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.457 r_dihedral_angle_3_deg 13.777 r_lrange_it 10.546 r_lrange_other 10.545 r_dihedral_angle_1_deg 7.629 r_scangle_it 6.122 r_scangle_other 6.122 r_dihedral_angle_2_deg 5.686 r_mcangle_it 4.689 r_mcangle_other 4.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.457 r_dihedral_angle_3_deg 13.777 r_lrange_it 10.546 r_lrange_other 10.545 r_dihedral_angle_1_deg 7.629 r_scangle_it 6.122 r_scangle_other 6.122 r_dihedral_angle_2_deg 5.686 r_mcangle_it 4.689 r_mcangle_other 4.688 r_scbond_it 3.809 r_scbond_other 3.808 r_mcbond_it 3.012 r_mcbond_other 3.012 r_angle_refined_deg 1.494 r_angle_other_deg 0.535 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.215 r_nbd_other 0.208 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.182 r_metal_ion_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.167 r_symmetry_nbd_refined 0.165 r_ncsr_local_group_1 0.112 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.069 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 4723 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing