3IR3

Crystal structure of human 3-hydroxyacyl-thioester dehydratase 2 (HTD2)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72770.5% jeff2001; 1.1M Na(malonate); 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.4664.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.88α = 90
b = 99.88β = 90
c = 77.72γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97930DiamondI04

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
11.9943.2599.40.0710.07110.83.629964
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.198.80.5010.5012.33.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1IQ61.9943.252843728437152099.30.171610.169920.20287RANDOM26.953
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]
-1.05-0.53-1.051.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.758
r_dihedral_angle_3_deg12.552
r_dihedral_angle_4_deg7.705
r_scangle_it6.392
r_scbond_it5.464
r_dihedral_angle_1_deg5.296
r_mcangle_it4.147
r_mcbond_it3.27
r_mcbond_other1.575
r_angle_refined_deg1.452
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.758
r_dihedral_angle_3_deg12.552
r_dihedral_angle_4_deg7.705
r_scangle_it6.392
r_scbond_it5.464
r_dihedral_angle_1_deg5.296
r_mcangle_it4.147
r_mcbond_it3.27
r_mcbond_other1.575
r_angle_refined_deg1.452
r_angle_other_deg1.072
r_chiral_restr0.087
r_bond_refined_d0.018
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1840
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms7

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling