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The internal aldimine form of the wild-type Salmonella Typhimurium Tryptophan Synthase in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor at the enzyme alpha-site, a single F6F molecule at the enzyme beta-site, and sodium ion at the metal coordination site at 1.55 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring
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 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.645 α = 90 b = 58.8 β = 95.13 c = 67.205 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 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HighFlux 2021-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.549 91.455 95.7 0.051 0.051 0.071 0.04 8.6 2.8 99219
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 1.55 1.63 73 0.299 0.299 0.476 0.312 2.4 1.7
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 (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 1.55 36.85 94154 4999 95.62 0.1738 0.1728 0.1739 0.194 0.1952 RANDOM 21.956
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] 0.02 -0.26 0.14 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.579 r_dihedral_angle_4_deg 20.974 r_dihedral_angle_3_deg 11.901 r_dihedral_angle_1_deg 5.948 r_angle_refined_deg 1.534 r_chiral_restr 0.099 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4857 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms 107
Software Software Software Name Purpose xia2 data reduction SCALA data scaling MOLREP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction