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Bacterial STING from Epilithonimonas lactis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M MOPSO/Bis-Tris pH 7.5,
90 mM lithium/sodium/potassium sulfate,
15 % (w/v) PEG 3000, 20 % (v/v) 1, 2, 4-Butanetriol, 1 % (w/v) NDSB 256
Crystal Properties Matthews coefficient Solvent content 2.34 47.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.981 α = 90 b = 56.981 β = 90 c = 187.551 γ = 120
Symmetry Space Group P 65 2 2
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 2022-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97625 NSRRC TPS 07A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.56 30 99.2 0.178 20.5 18.8 6344
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.56 2.65 95 1.09 1.43 8.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7EBL 2.568 23.873 5909 290 93.158 0.209 0.2073 0.244 40.987
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] -0.101 -0.05 -0.101 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.274 r_dihedral_angle_4_deg 24.323 r_dihedral_angle_3_deg 19.293 r_lrange_it 10.655 r_lrange_other 10.653 r_dihedral_angle_1_deg 7.543 r_scangle_it 7.434 r_scangle_other 7.432 r_mcangle_it 6.497 r_mcangle_other 6.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.274 r_dihedral_angle_4_deg 24.323 r_dihedral_angle_3_deg 19.293 r_lrange_it 10.655 r_lrange_other 10.653 r_dihedral_angle_1_deg 7.543 r_scangle_it 7.434 r_scangle_other 7.432 r_mcangle_it 6.497 r_mcangle_other 6.494 r_scbond_it 4.451 r_scbond_other 4.447 r_mcbond_it 4.079 r_mcbond_other 4.073 r_angle_refined_deg 1.406 r_angle_other_deg 1.189 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_refined 0.207 r_symmetry_nbd_other 0.206 r_nbd_other 0.201 r_symmetry_nbd_refined 0.183 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_other 0.132 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.058 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1235 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction