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Bacterial STING from Riemerella anatipestifer in complex with 3'3'-c-di-GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M Tris pH 8.5, 0.2 M calcium chloride dihydrate, 40 % v/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.92 35.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.51 α = 90 b = 40.99 β = 105.041 c = 36.196 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 2022-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97624 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 1.46 30 99.3 0.054 30.227 6.2 24248
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 1.46 1.51 95 0.489 2.92 4.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7EBD 1.462 22.805 24109 1219 98.328 0.183 0.1813 0.1815 0.2095 0.2098 17.222
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] 0.204 0.018 -0.23 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.234 r_dihedral_angle_4_deg 19.3 r_dihedral_angle_3_deg 12.417 r_dihedral_angle_1_deg 6.728 r_lrange_it 5.786 r_lrange_other 5.736 r_scangle_it 4.475 r_scangle_other 4.473 r_scbond_other 2.958 r_scbond_it 2.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.234 r_dihedral_angle_4_deg 19.3 r_dihedral_angle_3_deg 12.417 r_dihedral_angle_1_deg 6.728 r_lrange_it 5.786 r_lrange_other 5.736 r_scangle_it 4.475 r_scangle_other 4.473 r_scbond_other 2.958 r_scbond_it 2.954 r_mcangle_other 2.703 r_mcangle_it 2.701 r_mcbond_it 1.768 r_mcbond_other 1.76 r_angle_refined_deg 1.437 r_angle_other_deg 1.37 r_nbd_refined 0.227 r_nbd_other 0.181 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.176 r_symmetry_xyhbond_nbd_refined 0.174 r_xyhbond_nbd_refined 0.164 r_symmetry_nbd_refined 0.162 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.074 r_metal_ion_refined 0.066 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1286 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction