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Quinonoid intermediate of Citrobacter freundii tyrosine phenol-lyase formed with alanine
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 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 50MM K-PHOSPHATE PH 8.0, 0.5 MM PLP, 1MM 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. QUINONOID INTERMEDIATE WITH ALANINE WAS PREPARED BY SOAKING THE TPL CRYSTALS FOR 5 MIN 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 L-ALA.
Crystal Properties Matthews coefficient Solvent content 2.76 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.846 α = 90 b = 143.687 β = 90 c = 59.618 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE MARRESEARCH MIRRORS 1995-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.89 20 97.3 0.07 12.2 3.7 89055 2 18.9
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 1.89 1.93 87.5 0.36 2.3
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 1.89 20 87930 1065 96.7 0.158 0.157 0.1585 0.198 0.2011 RANDOM 22.89
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] 0.03 -1.24 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.308 r_dihedral_angle_3_deg 14.295 r_dihedral_angle_4_deg 13.548 r_dihedral_angle_1_deg 6.178 r_scangle_it 5.824 r_scbond_it 4.188 r_mcangle_it 2.18 r_angle_refined_deg 1.438 r_mcbond_it 1.393 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.308 r_dihedral_angle_3_deg 14.295 r_dihedral_angle_4_deg 13.548 r_dihedral_angle_1_deg 6.178 r_scangle_it 5.824 r_scbond_it 4.188 r_mcangle_it 2.18 r_angle_refined_deg 1.438 r_mcbond_it 1.393 r_nbtor_refined 0.308 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 7214 Nucleic Acid Atoms Solvent Atoms 966 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing