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Crystal structure of the Fe(II)/alpha-ketoglutarate dependent taurine dioxygenase from Pseudomonas putida KT2440
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PVJ PDB entry 3PVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 reservoir solution: 20 % (w/v) PEG 5,000 MME, 0.1 M Bis Tris/HCl (pH 6.5)
protein solution: 21 mg/ml protein in 25 mM Tris/HCl (pH 7.7) containing 10 mM taurine, 0.1 (NH4)2SO4 and 20 % (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.83 56.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.889 α = 90 b = 101.85 β = 90 c = 162.771 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 IMAGE PLATE MARRESEARCH 2006-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 30 99.7 0.088 18.4 4.6 44171 44029 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.7 99.7 0.595 4.6 4669
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB entry 3PVJ 2.6 28.78 1.99 44004 2201 99.72 0.1864 0.1829 0.1757 0.2544 0.246 random
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] 15.8789 -6.0157 -9.8632
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.976 f_angle_d 1.158 f_chiral_restr 0.073 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8764 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing PHENIX refinement XDS data reduction XDS data scaling