5TID

X-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 5 in complex with octanoic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529320-25% PEG-5000, 100 mM homopipes, 3 mM octanoic acid
Crystal Properties
Matthews coefficientSolvent content
2.2244.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.716α = 90
b = 55.177β = 105.18
c = 42.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-07-16MSINGLE 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
11.25099.50.0560.05613.23.756148
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)
11.21.397.30.30232.2

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 REPLACEMENTTHROUGHOUT5TIC1.240.8553269287999.40.159290.158320.17746RANDOM11.811
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]
0.1-0.20.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.57
r_dihedral_angle_4_deg17.042
r_dihedral_angle_3_deg15.172
r_long_range_B_refined6.622
r_long_range_B_other6.204
r_dihedral_angle_1_deg5.477
r_scangle_other4.959
r_scbond_it3.218
r_scbond_other3.216
r_mcangle_other1.892
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.57
r_dihedral_angle_4_deg17.042
r_dihedral_angle_3_deg15.172
r_long_range_B_refined6.622
r_long_range_B_other6.204
r_dihedral_angle_1_deg5.477
r_scangle_other4.959
r_scbond_it3.218
r_scbond_other3.216
r_mcangle_other1.892
r_mcangle_it1.887
r_angle_refined_deg1.737
r_mcbond_it1.269
r_mcbond_other1.244
r_angle_other_deg0.838
r_chiral_restr0.118
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.001
r_bond_other_d
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1410
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing