5TIC

X-ray structure of wild-type E. coli Acyl-CoA thioesterase I at pH 5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U8U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529322-26% PEG-5000, 100 mM homopipesa
Crystal Properties
Matthews coefficientSolvent content
2.1943.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.922α = 90
b = 82.124β = 90.44
c = 53.903γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-07-04MSINGLE 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
11.6550980.0680.06810.63.742019
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)
11.651.7594.90.3781.92.6

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 REPLACEMENTTHROUGHOUT1u8u1.655039926209398.010.188040.186190.222RANDOM20.632
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]
-0.010.230.67-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.318
r_dihedral_angle_4_deg17.796
r_dihedral_angle_3_deg15.169
r_long_range_B_refined6.346
r_long_range_B_other6.093
r_dihedral_angle_1_deg5.836
r_scangle_other4.862
r_scbond_it3.189
r_scbond_other3.188
r_mcangle_it2.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.318
r_dihedral_angle_4_deg17.796
r_dihedral_angle_3_deg15.169
r_long_range_B_refined6.346
r_long_range_B_other6.093
r_dihedral_angle_1_deg5.836
r_scangle_other4.862
r_scbond_it3.189
r_scbond_other3.188
r_mcangle_it2.95
r_mcangle_other2.949
r_mcbond_it2.009
r_mcbond_other1.979
r_angle_refined_deg1.768
r_angle_other_deg0.943
r_chiral_restr0.114
r_bond_refined_d0.012
r_gen_planes_refined0.008
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2823
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing