5TIE

x-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 7.5 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 DROP7.529324-28% PEG-5000, 100 mM Hepes, 3 mM octanoic acid
Crystal Properties
Matthews coefficientSolvent content
2.2244.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.759α = 90
b = 55.306β = 104.91
c = 42.22γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-07-24MSINGLE 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
11.155098.20.0450.045112.362723
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)
11.151.2591.80.212.71.3

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 SYNTHESISTHROUGHOUT5TID1.1540.859641308298.170.130740.129110.16253RANDOM12.293
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]
-0.01-0.15-0.020.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.271
r_sphericity_free21.684
r_dihedral_angle_3_deg12.333
r_dihedral_angle_4_deg12.189
r_sphericity_bonded8.633
r_rigid_bond_restr7.135
r_dihedral_angle_1_deg5.567
r_long_range_B_refined3.757
r_scangle_other3.149
r_long_range_B_other3.051
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.271
r_sphericity_free21.684
r_dihedral_angle_3_deg12.333
r_dihedral_angle_4_deg12.189
r_sphericity_bonded8.633
r_rigid_bond_restr7.135
r_dihedral_angle_1_deg5.567
r_long_range_B_refined3.757
r_scangle_other3.149
r_long_range_B_other3.051
r_scbond_it2.981
r_scbond_other2.979
r_angle_refined_deg1.904
r_mcangle_it1.527
r_mcangle_other1.526
r_mcbond_other1.306
r_mcbond_it1.304
r_angle_other_deg0.884
r_chiral_restr0.124
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1435
Nucleic Acid Atoms
Solvent Atoms381
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing