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Crystal structure of Alpha-ketoglutarate-dependent taurine dioxygenase from Mycobacterium avium, native form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OIJ PDB ENTRY 1OIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 Internal tracking number 218640E10. PACT screen condition E10:
0.2 M Na/K Phosphate, 20% PEG3350, MyavA.01188.b.A1
PW28977 at 28.9mg/ml. Cryoprotection: 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.49 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.95 α = 90 b = 105.31 β = 90 c = 89.25 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 RIGAKU SATURN 944+ 2011-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.541780
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 2.05 41.09 99.7 0.081 15.84 5.7 42701 42570 -3 28.296
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 2.05 2.1 99.3 0.424 3.1 3.4 3124
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MR THROUGHOUT PDB ENTRY 1OIJ 2.05 37.78 42570 42393 2139 99.27 0.173 0.173 0.171 0.2179 0.2 0.2383 RANDOM 25.258
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] 1.04 -0.15 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.769 r_dihedral_angle_4_deg 16.796 r_dihedral_angle_3_deg 11.554 r_dihedral_angle_1_deg 6.296 r_scangle_it 3.269 r_scbond_it 2.07 r_angle_refined_deg 1.365 r_mcangle_it 1.252 r_angle_other_deg 0.869 r_mcbond_it 0.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.769 r_dihedral_angle_4_deg 16.796 r_dihedral_angle_3_deg 11.554 r_dihedral_angle_1_deg 6.296 r_scangle_it 3.269 r_scbond_it 2.07 r_angle_refined_deg 1.365 r_mcangle_it 1.252 r_angle_other_deg 0.869 r_mcbond_it 0.702 r_mcbond_other 0.195 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3832 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 17
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction