3O3O

(R)-2-hydroxyisocaproyl-CoA dehydratase in complex with (R)-2-hydroxyisocaproate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O3MPDB entry 3O3M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5290The dehydratase was cocrystallized by incubation with 5 mM (R)-2-hydroxyisocaproate 10 minutes prior to crystallization. Reservoir solution: 23 % PEG 3350, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.3146.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.309α = 90
b = 85.584β = 90
c = 149.508γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225Double crystal monochromator with 2 sets of mirrors2008-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.99430960.099.253.65744055143-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.9942.188.90.2773.042.4

Refinement

Statistics
Diffraction IDStructure Solution 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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 3O3M229.0721.995771255133275896.080.20640.20380.2571
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]
10.8887-8.8265-2.0622
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.436
f_angle_d1.347
f_chiral_restr0.076
f_bond_d0.01
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6135
Nucleic Acid Atoms
Solvent Atoms766
Heterogen Atoms26

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling