2YHK | pdb_00002yhk

D214A mutant of tyrosine phenol-lyase from Citrobacter freundii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EZ1PDB ENTRY 2EZ1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293THE CRYSTALS WERE GROWN AT 293 K BY THE HANGING DROP VAPOR DIFFUSION TECHNIQUE BY MIXING 2 UL OF THE PROTEIN SOLUTION, 18-20 MG/ML, WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 50 MMOL/L TRIETHANOLAMINE BUFFER PH 8.0, 0.4-0.8 MOL/L KCL, 0.35-0.38 G/ML PEG 5000 MME, 5 MMOL/L PYRIDOXAL-5-PHOSPHATE, AND 2 MMOL/L DITHIOTHREITOL.
Crystal Properties
Matthews coefficientSolvent content
2.755

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.605α = 90
b = 142.705β = 90
c = 59.412γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH SX-165MIRRORS2005-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
11.9125990.07154.587110-124.4
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)
11.911.97990.53.14.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2EZ11.912585457128398.560.156040.155710.180.177110.19RANDOM32.732
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]
-0.36-1.581.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.425
r_dihedral_angle_4_deg15.088
r_dihedral_angle_3_deg14.206
r_dihedral_angle_1_deg6.016
r_scangle_it5.984
r_scbond_it4.032
r_mcangle_it2.259
r_mcbond_it1.427
r_angle_refined_deg1.393
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.425
r_dihedral_angle_4_deg15.088
r_dihedral_angle_3_deg14.206
r_dihedral_angle_1_deg6.016
r_scangle_it5.984
r_scbond_it4.032
r_mcangle_it2.259
r_mcbond_it1.427
r_angle_refined_deg1.393
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 Atoms7202
Nucleic Acid Atoms
Solvent Atoms746
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing