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Bacterial STING from Larkinella arboricola in complex with 3'3'-c-di-GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M Imidazole pH 7.5, 0.1 M Sodium chloride, 20% v/v Jeffamine ED-2001 pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.987 α = 90 b = 72.489 β = 90 c = 231.066 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 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 2.72 30 96.5 0.099 23.3 10.3 30140 45.98
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 2.72 2.82 1.526 8.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.73 29.31 25497 1343 85.7 0.21172 0.20883 0.2085 0.26598 0.2615 RANDOM 57.487
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] 0.06 0.09 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.733 r_dihedral_angle_3_deg 16.791 r_dihedral_angle_4_deg 14.343 r_long_range_B_other 11.236 r_long_range_B_refined 11.235 r_mcangle_it 7.095 r_mcangle_other 7.095 r_scangle_other 6.485 r_dihedral_angle_1_deg 6.053 r_mcbond_it 4.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.733 r_dihedral_angle_3_deg 16.791 r_dihedral_angle_4_deg 14.343 r_long_range_B_other 11.236 r_long_range_B_refined 11.235 r_mcangle_it 7.095 r_mcangle_other 7.095 r_scangle_other 6.485 r_dihedral_angle_1_deg 6.053 r_mcbond_it 4.183 r_mcbond_other 4.176 r_scbond_it 3.802 r_scbond_other 3.802 r_angle_other_deg 2.184 r_angle_refined_deg 1.286 r_chiral_restr 0.057 r_bond_other_d 0.033 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8812 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHENIX phasing HKL-2000 data reduction