3S2Z

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PF8PDB entry 3PF8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.1 M TRIS, 0.2 M LITHIUM SULPHATE, 30% PEG4K, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.244.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.318α = 90
b = 84.168β = 97.56
c = 87.604γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2010-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

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
11.755099.70.04721.864.151281514282
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)
11.751.7897.60.4623.32520

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 3PF81.765048659261598.910.145960.142580.20862RANDOM35.29
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]
-0.01-1.03-2.071.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.432
r_dihedral_angle_4_deg21.877
r_dihedral_angle_3_deg13.731
r_scangle_it7.016
r_dihedral_angle_1_deg6.059
r_scbond_it4.945
r_mcangle_it2.925
r_rigid_bond_restr2.533
r_mcbond_it1.901
r_angle_refined_deg1.812
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.432
r_dihedral_angle_4_deg21.877
r_dihedral_angle_3_deg13.731
r_scangle_it7.016
r_dihedral_angle_1_deg6.059
r_scbond_it4.945
r_mcangle_it2.925
r_rigid_bond_restr2.533
r_mcbond_it1.901
r_angle_refined_deg1.812
r_chiral_restr0.132
r_bond_refined_d0.023
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 Atoms3916
Nucleic Acid Atoms
Solvent Atoms432
Heterogen Atoms42

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling