2VSS

Wild-type Hydroxycinnamoyl-CoA hydratase lyase in complex with acetyl- CoA and vanillin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1PROTEIN CONCENTRATION OF 10 MG ML-1 IN 11% (W/V) PEG 20 000 DA WITH 8% (V/V) PEG 550 DA MONOMETHYL ETHER, 0.8 M SODIUM FORMATE AND 0.2% (V/V) BUTANE 1,4-DIOL IN 0.05 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID BUFFER PH 5.6. 10MM FERULOYL-COA
Crystal Properties
Matthews coefficientSolvent content
2.346.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.223α = 90
b = 130.595β = 90
c = 144.663γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2872007-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.2297.1391.50.1295.2739672
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)
12.222.2750.30.372.94.7

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 2J5I2.2297.1373967393391.50.1860.1830.242RANDOM37.85
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]
-0.39-1.842.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.425
r_dihedral_angle_4_deg22.714
r_dihedral_angle_3_deg15.883
r_dihedral_angle_1_deg6.949
r_scangle_it4.142
r_scbond_it2.861
r_angle_refined_deg1.966
r_mcangle_it1.58
r_mcbond_it1.069
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.425
r_dihedral_angle_4_deg22.714
r_dihedral_angle_3_deg15.883
r_dihedral_angle_1_deg6.949
r_scangle_it4.142
r_scbond_it2.861
r_angle_refined_deg1.966
r_mcangle_it1.58
r_mcbond_it1.069
r_nbtor_refined0.305
r_symmetry_vdw_refined0.303
r_symmetry_hbond_refined0.251
r_nbd_refined0.215
r_xyhbond_nbd_refined0.152
r_chiral_restr0.124
r_bond_refined_d0.023
r_gen_planes_refined0.008
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_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 Atoms11344
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms215

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing