2VX2

Crystal structure of human enoyl Coenzyme A hydratase domain- containing protein 3 (ECHDC3)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.20M NA(FORM); 0.1M BTPROP PH 8.5, 20.0% PEG350, 10.0% ETGLY
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 235.756α = 90
b = 135.296β = 98.84
c = 83.871γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
12.311799.60.089.72.81181522
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)
12.32.4699.50.522.32.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1UIY2.3117.04108794576799.40.1720.170.22RANDOM17.09
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]
-0.350.69-3.734.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.816
r_dihedral_angle_4_deg19.132
r_dihedral_angle_3_deg15.145
r_dihedral_angle_1_deg5.93
r_scangle_it3.421
r_scbond_it2.179
r_angle_refined_deg1.633
r_mcangle_it1.169
r_angle_other_deg1.066
r_mcbond_it0.665
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.816
r_dihedral_angle_4_deg19.132
r_dihedral_angle_3_deg15.145
r_dihedral_angle_1_deg5.93
r_scangle_it3.421
r_scbond_it2.179
r_angle_refined_deg1.633
r_mcangle_it1.169
r_angle_other_deg1.066
r_mcbond_it0.665
r_chiral_restr0.095
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16927
Nucleic Acid Atoms
Solvent Atoms573
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing