5TIF

x-ray structure of acyl-CoA thioesterase I, TesA, triple mutant M141L/Y145K/L146K in complex with octanoic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TID 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529320-25% PEG-5000, 100 mM homopipes, 3 mM octanoic acid
Crystal Properties
Matthews coefficientSolvent content
2.1943.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.5α = 90
b = 55β = 104.9
c = 42γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
10.975097.80.060.00611.84.1102836
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.971.0792.80.2782.42.3

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5tid0.9740.5997699513797.830.122760.121980.13736RANDOM16.085
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]
0.040.18-0.02-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free76.848
r_dihedral_angle_2_deg36.083
r_sphericity_bonded19.723
r_dihedral_angle_4_deg17.684
r_dihedral_angle_3_deg13.351
r_long_range_B_refined9.682
r_long_range_B_other9.682
r_rigid_bond_restr7.68
r_scbond_it7.085
r_scbond_other7.085
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free76.848
r_dihedral_angle_2_deg36.083
r_sphericity_bonded19.723
r_dihedral_angle_4_deg17.684
r_dihedral_angle_3_deg13.351
r_long_range_B_refined9.682
r_long_range_B_other9.682
r_rigid_bond_restr7.68
r_scbond_it7.085
r_scbond_other7.085
r_scangle_other6.679
r_dihedral_angle_1_deg6.024
r_mcangle_other2.675
r_mcangle_it2.661
r_mcbond_it2.136
r_mcbond_other2.028
r_angle_refined_deg2.012
r_angle_other_deg1.533
r_chiral_restr0.138
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1440
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing