2HW5

The crystal structure of human enoyl-coenzyme A (CoA) hydratase short chain 1, ECHS1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DUBPDB ENTRY 1DUB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.2M sodium formate, 0.1M Bis-Tris propane, 20 % PEG3350, 10 % Ethylene Glycol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7755.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.554α = 90
b = 97.344β = 90
c = 231.796γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9791SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.553097.86669666696
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.6499.7

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DUB2.5529.66326563265335997.540.216140.216140.214250.25165RANDOM63.522
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]
4.79-2.73-2.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.973
r_dihedral_angle_4_deg17.044
r_dihedral_angle_3_deg15.344
r_dihedral_angle_1_deg5.821
r_scangle_it1.715
r_angle_refined_deg1.116
r_scbond_it1.061
r_angle_other_deg0.846
r_mcangle_it0.684
r_mcbond_it0.405
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.973
r_dihedral_angle_4_deg17.044
r_dihedral_angle_3_deg15.344
r_dihedral_angle_1_deg5.821
r_scangle_it1.715
r_angle_refined_deg1.116
r_scbond_it1.061
r_angle_other_deg0.846
r_mcangle_it0.684
r_mcbond_it0.405
r_nbd_refined0.207
r_symmetry_vdw_other0.2
r_nbd_other0.176
r_nbtor_refined0.174
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.135
r_nbtor_other0.086
r_symmetry_vdw_refined0.079
r_mcbond_other0.064
r_chiral_restr0.062
r_bond_refined_d0.009
r_xyhbond_nbd_other0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
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 Atoms11455
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing