2YCN

Y71F mutant of tyrosine phenol-lyase from Citrobacter freundii in complex with quinonoid intermediate formed with 3-fluoro-L-tyrosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EZ2PDB ENTRY 2EZ2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293CRYSTALS WERE GROWN AT 277 AND 293 K USING THE HANGING DROP VAPOR DIFFUSION METHOD. THE BEST CRYSTALS WERE OBTAINED BY MIXING 2 UL OF THE PROTEIN SOLUTION (18-20 MG/ML) CONTAINING 50 MM K-PHOSPHATE PH 8.0, 0.5 MM PLP, 1 MM DDT WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 50 MM TRIETHANOLAMINE BUFFER (PH 8.0), 0.5 MM PLP, 2 MM DDT, 0.4 M KCL, AND 35-38% (W/V) POLY(ETHYLENE GLYCOL) 5000 MONOMETHYL ETHER. COMPLEX OF Y71F TPL WITH 3-FLUORO-L-TYROSINE WAS PREPARED BY SOAKING CRYSTALS IN THE STABILIZING SOLUTION CONTAINING 10 MM 3- FLUORO-L-TYROSINE FOR ABOUT 30 SECONDS.
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.635α = 90
b = 144.397β = 90
c = 59.66γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2002-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.0417960.0513.7371319-10
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)
12.042.09840.353.21.9

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 2EZ22.0498.0670272104795.670.164050.163390.20886RANDOM36.792
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]
0.21-1.211
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.211
r_dihedral_angle_3_deg14.819
r_dihedral_angle_4_deg12.093
r_dihedral_angle_1_deg6.343
r_scangle_it5.667
r_scbond_it4.087
r_mcangle_it2.188
r_angle_refined_deg1.383
r_mcbond_it1.38
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.211
r_dihedral_angle_3_deg14.819
r_dihedral_angle_4_deg12.093
r_dihedral_angle_1_deg6.343
r_scangle_it5.667
r_scbond_it4.087
r_mcangle_it2.188
r_angle_refined_deg1.383
r_mcbond_it1.38
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.006
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_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 Atoms7222
Nucleic Acid Atoms
Solvent Atoms745
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing