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Crystal structure of bovine Thiosulfate sulfurtransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 PEG 6000, Tris, calcium chloride dihydrate
Crystal Properties Matthews coefficient Solvent content 2.39 48.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.857 α = 90 b = 49.506 β = 98.504 c = 41.863 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 2022-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033220 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.5 38.86 96.2 0.056 0.999 27.9 12.8 47923
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.176 0.989
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 FREE R-VALUE 1.5 38.86 47921 2367 95.834 0.147 0.1463 0.1464 0.1628 0.1629 12.056
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] -0.253 0.155 0.066 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.567 r_dihedral_angle_4_deg 14.06 r_dihedral_angle_3_deg 10.34 r_dihedral_angle_1_deg 6.295 r_lrange_it 4.323 r_lrange_other 4.26 r_scangle_it 3.479 r_scangle_other 3.476 r_scbond_it 2.305 r_scbond_other 2.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.567 r_dihedral_angle_4_deg 14.06 r_dihedral_angle_3_deg 10.34 r_dihedral_angle_1_deg 6.295 r_lrange_it 4.323 r_lrange_other 4.26 r_scangle_it 3.479 r_scangle_other 3.476 r_scbond_it 2.305 r_scbond_other 2.296 r_angle_refined_deg 1.782 r_mcangle_other 1.671 r_mcangle_it 1.669 r_angle_other_deg 1.569 r_mcbond_it 1.124 r_mcbond_other 1.12 r_symmetry_nbd_refined 0.37 r_nbd_other 0.314 r_nbd_refined 0.238 r_nbtor_refined 0.188 r_symmetry_nbd_other 0.177 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.1 r_symmetry_xyhbond_nbd_refined 0.099 r_metal_ion_refined 0.095 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2317 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing