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D214A mutant of tyrosine phenol-lyase from Citrobacter freundii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EZ1 PDB ENTRY 2EZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 THE 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 coefficient Solvent content 2.7 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.605 α = 90 b = 142.705 β = 90 c = 59.412 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 100 CCD MARRESEARCH SX-165 MIRRORS 2005-05-02 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 1.91 25 99 0.07 15 4.5 87110 -1 24.4
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 1.91 1.97 99 0.5 3.1 4.2
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2EZ1 1.91 25 85457 1283 98.56 0.15604 0.15571 0.177 0.17711 0.195 RANDOM 32.732
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 -1.58 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.425 r_dihedral_angle_4_deg 15.088 r_dihedral_angle_3_deg 14.206 r_dihedral_angle_1_deg 6.016 r_scangle_it 5.984 r_scbond_it 4.032 r_mcangle_it 2.259 r_mcbond_it 1.427 r_angle_refined_deg 1.393 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.425 r_dihedral_angle_4_deg 15.088 r_dihedral_angle_3_deg 14.206 r_dihedral_angle_1_deg 6.016 r_scangle_it 5.984 r_scbond_it 4.032 r_mcangle_it 2.259 r_mcbond_it 1.427 r_angle_refined_deg 1.393 r_chiral_restr 0.1 r_bond_refined_d 0.015 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 7202 Nucleic Acid Atoms Solvent Atoms 746 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing