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Bacterial STING from Epilithonimonas lactis in complex with 3'3'-c-di-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M MES pH 6.0, 0.1 M Sodium chloride, 30 % v/v PEG 3500
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.171 α = 90 b = 52.713 β = 114.883 c = 88.932 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 2022-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97626 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 2.55 30 96.5 0.121 14.1 6.3 20886
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 2.55 2.64 0.578 2.3 5.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.553 25.769 19584 962 89.818 0.197 0.195 0.2276 0.2137 45.432
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] 0.439 0.571 -0.735 -0.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.829 r_dihedral_angle_3_deg 18.753 r_dihedral_angle_4_deg 18.662 r_lrange_other 10.578 r_lrange_it 10.577 r_dihedral_angle_1_deg 6.597 r_mcangle_it 6.585 r_mcangle_other 6.584 r_scangle_it 6.455 r_scangle_other 6.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.829 r_dihedral_angle_3_deg 18.753 r_dihedral_angle_4_deg 18.662 r_lrange_other 10.578 r_lrange_it 10.577 r_dihedral_angle_1_deg 6.597 r_mcangle_it 6.585 r_mcangle_other 6.584 r_scangle_it 6.455 r_scangle_other 6.452 r_mcbond_it 3.972 r_mcbond_other 3.972 r_scbond_it 3.881 r_scbond_other 3.878 r_angle_other_deg 2.272 r_angle_refined_deg 1.438 r_nbd_other 0.288 r_symmetry_nbd_other 0.231 r_symmetry_nbd_refined 0.217 r_nbd_refined 0.209 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_other 0.124 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.072 r_bond_other_d 0.034 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5151 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction