5BW6

Tryptophan Synthase from Salmonella typhimurium in complex with a single molecule of 2-({[4-(trifluoromethoxy)phenyl]carbonyl}amino)ethyl dihydrogen phosphate (F6) in the alpha-site.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WX2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.829850mM Bicine-NaOH, pH 7.8, containing 50mM NaCl, 2mM spermine, and 10% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.5251.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.03α = 90
b = 58.9β = 94.91
c = 67.23γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VariMax2013-03-01MSINGLE 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)CC (Half)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
11.822072.80.0430.0430.0560.0350.99913.12.14657346573
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.9269.70.4540.0180.0140.75622.16445

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 REPLACEMENTTHROUGHOUT4WX21.8219.8344334223772.580.17050.16820.2143RANDOM25.879
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]
-0.04-0.030.05-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.417
r_dihedral_angle_4_deg18.657
r_dihedral_angle_3_deg14.47
r_dihedral_angle_1_deg6.187
r_angle_refined_deg1.655
r_mcangle_it1.238
r_scbond_it0.875
r_mcbond_it0.705
r_chiral_restr0.108
r_bond_refined_d0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.417
r_dihedral_angle_4_deg18.657
r_dihedral_angle_3_deg14.47
r_dihedral_angle_1_deg6.187
r_angle_refined_deg1.655
r_mcangle_it1.238
r_scbond_it0.875
r_mcbond_it0.705
r_chiral_restr0.108
r_bond_refined_d0.014
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4924
Nucleic Acid Atoms
Solvent Atoms673
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction