7LY8

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HT3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.829850 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.652.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.645α = 90
b = 58.8β = 95.13
c = 67.205γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VariMax HighFlux2021-01-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.54991.45595.70.0510.0510.0710.048.62.899219
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)RedundancyNumber Unique Reflections (All)
11.551.63730.2990.2990.4760.3122.41.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4HT31.5536.8594154499995.620.17380.17280.194RANDOM21.956
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]
0.02-0.260.14-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.579
r_dihedral_angle_4_deg20.974
r_dihedral_angle_3_deg11.901
r_dihedral_angle_1_deg5.948
r_angle_refined_deg1.534
r_chiral_restr0.099
r_gen_planes_refined0.009
r_bond_refined_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4857
Nucleic Acid Atoms
Solvent Atoms627
Heterogen Atoms107

Software

Software
Software NamePurpose
xia2data reduction
SCALAdata scaling
MOLREPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction