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The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site, two molecules of F6F inhibitor at the enzyme alpha-site and another F6F molecule at the enzyme beta-site at 1.40 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.259 α = 90 b = 58.9 β = 94.82 c = 67.23 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 PILATUS 6M 2020-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9793 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.4 91.306 97.1 0.061 0.061 0.081 0.041 8.8 3.8 136186 136186
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 82.2 0.438 0.438 0.042 0.021 1.7 2.9
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 (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 4HT3 1.4 36.79 129318 6868 97 0.138 0.136 0.135 0.177 0.1761 RANDOM 20.67
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 0.07 -0.73 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.697 r_dihedral_angle_4_deg 19.168 r_dihedral_angle_3_deg 12.295 r_rigid_bond_restr 6.401 r_dihedral_angle_1_deg 6.041 r_angle_refined_deg 1.406 r_chiral_restr 0.099 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.697 r_dihedral_angle_4_deg 19.168 r_dihedral_angle_3_deg 12.295 r_rigid_bond_restr 6.401 r_dihedral_angle_1_deg 6.041 r_angle_refined_deg 1.406 r_chiral_restr 0.099 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4930 Nucleic Acid Atoms Solvent Atoms 892 Heterogen Atoms 239
Software Software Software Name Purpose REFMAC refinement xia2 data reduction SCALA data scaling MOLREP phasing DM phasing PDB_EXTRACT data extraction