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Bacterial STING from Riemerella anatipestifer
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/MES pH 6.5, 0.1 M carboxylic acids, 20% v/v Ethylene glycol, 10 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.265 α = 90 b = 60.121 β = 90 c = 118.823 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 CCD ADSC QUANTUM 210 2021-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00000 NSRRC BL13B1
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 2.089 30 98.3 0.042 43.126 7.1 22890
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 2.089 2.18 0.301
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 THROUGHOUT 2.089 25.957 22788 1140 97.643 0.192 0.1893 0.1943 0.2387 0.2418 33.11
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] -0.135 0.533 -0.398
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.362 r_dihedral_angle_3_deg 13.729 r_dihedral_angle_4_deg 13.275 r_lrange_it 8.2 r_lrange_other 8.063 r_dihedral_angle_1_deg 6.043 r_scangle_it 5.644 r_scangle_other 5.642 r_mcangle_it 4.29 r_mcangle_other 4.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.362 r_dihedral_angle_3_deg 13.729 r_dihedral_angle_4_deg 13.275 r_lrange_it 8.2 r_lrange_other 8.063 r_dihedral_angle_1_deg 6.043 r_scangle_it 5.644 r_scangle_other 5.642 r_mcangle_it 4.29 r_mcangle_other 4.289 r_scbond_it 3.573 r_scbond_other 3.572 r_mcbond_it 2.928 r_mcbond_other 2.919 r_angle_other_deg 1.438 r_angle_refined_deg 1.395 r_nbd_other 0.257 r_xyhbond_nbd_refined 0.222 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.204 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.17 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.056 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2553 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing