3PFB

Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with ethylferulate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherCrystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.1 M Tris pH 8.5, 0.2 M ammonium sulphate, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2244.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.26α = 90
b = 83.891β = 98.21
c = 88.947γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCmirrors2009-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
11.585073.10.04631.2125248752487-3
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)
11.581.6121.60.263.091.3769

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 REPLACEMENTTHROUGHOUTCrystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant1.5844.249803267373.060.216090.21130.30439RANDOM26.599
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]
0.650.04-1.610.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.66
r_dihedral_angle_4_deg20.668
r_dihedral_angle_3_deg15.05
r_dihedral_angle_1_deg6.86
r_scangle_it5.708
r_scbond_it4.285
r_mcangle_it2.393
r_rigid_bond_restr2.268
r_angle_refined_deg1.933
r_mcbond_it1.698
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.66
r_dihedral_angle_4_deg20.668
r_dihedral_angle_3_deg15.05
r_dihedral_angle_1_deg6.86
r_scangle_it5.708
r_scbond_it4.285
r_mcangle_it2.393
r_rigid_bond_restr2.268
r_angle_refined_deg1.933
r_mcbond_it1.698
r_chiral_restr0.128
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3908
Nucleic Acid Atoms
Solvent Atoms907
Heterogen Atoms52

Software

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