2H4U

Crystal Structure of Human Thioesterase Superfamily Member 2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729320 % PEG 3350, 0.2M Na/K phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3748.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.05α = 90
b = 90.97β = 90
c = 114.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMirrors2006-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.976ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.210099.60.07817.587.23094830821-334.6
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)
2.22.499.80.287.57.36965

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1WN32.219.5523089429216153899.550.219690.216980.27189RANDOM17.43
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]
-0.02-0.060.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.82
r_dihedral_angle_4_deg18.952
r_dihedral_angle_3_deg18.149
r_dihedral_angle_1_deg6.489
r_scangle_it2.867
r_scbond_it1.777
r_angle_refined_deg1.591
r_mcangle_it1.141
r_mcbond_it0.742
r_symmetry_hbond_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.82
r_dihedral_angle_4_deg18.952
r_dihedral_angle_3_deg18.149
r_dihedral_angle_1_deg6.489
r_scangle_it2.867
r_scbond_it1.777
r_angle_refined_deg1.591
r_mcangle_it1.141
r_mcbond_it0.742
r_symmetry_hbond_refined0.3
r_nbtor_refined0.296
r_nbd_refined0.235
r_symmetry_vdw_refined0.226
r_xyhbond_nbd_refined0.168
r_chiral_restr0.104
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3662
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
XDSdata scaling
MOLREPphasing