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F448H mutant of tyrosine phenol-lyase from Citrobacter freundii in complex with quinonoid intermediate formed with 3-fluoro-L-tyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EZ2 PDB ENTRY 2EZ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 CRYSTALS OF THE C. FREUNDII F448H TPL 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. THE QUINONOID INTERMEDIATE WITH 3-FLUORO-L-TYROSINE WAS PREPARED BY SOAKING THE TPL CRYSTALS FOR ABOUT 30 SECONDS IN THE STABILIZATION SOLUTION CONTAINING 40% POLY(ETHYLENE GLYCOL) 5000 MONOMETHYL ETHER, 50 MM TRIETHANOLAMINE BUFFER (PH 8.0), 0.25 M KCL, 0.2 MM PLP, 0.5 MM DTT AND 10 MM 3-FLUORO-L-TYROSINE. CRYSTALS WERE FROZEN DIRECTLY FROM THE SOAKING SOLUTION.
Crystal Properties Matthews coefficient Solvent content 2.8 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.423 α = 90 b = 143.757 β = 90 c = 118.543 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH SX-165 MIRRORS 2005-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 30 99 0.09 7.5 4.7 154478 -10
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99 0.53 2.5 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2EZ2 2 30 152931 1547 98.66 0.14114 0.1408 0.1568 0.1747 0.1841 RANDOM 23.853
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] -0.71 -1.03 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.579 r_dihedral_angle_4_deg 14.197 r_dihedral_angle_3_deg 13.773 r_dihedral_angle_1_deg 6.297 r_scangle_it 5.505 r_scbond_it 3.752 r_mcangle_it 1.906 r_angle_refined_deg 1.304 r_mcbond_it 1.158 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.579 r_dihedral_angle_4_deg 14.197 r_dihedral_angle_3_deg 13.773 r_dihedral_angle_1_deg 6.297 r_scangle_it 5.505 r_scbond_it 3.752 r_mcangle_it 1.906 r_angle_refined_deg 1.304 r_mcbond_it 1.158 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 14444 Nucleic Acid Atoms Solvent Atoms 1861 Heterogen Atoms 393
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing