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Crystal structure of an alpha-ketoglutarate-dependent taurine dioxygenase from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R1J PDB entry 3R1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 MysmA.01188.a.A1 PS00650 at 20 mg/mL against Morpheus condition A2, 10% PEG 8000, 20% ethylene glycol, 30 mM MgCl, 30 mM CaCl2, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 233128a2, unique puck ID oqa0-7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.38 48.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.01 α = 90 b = 166.68 β = 90.57 c = 99.72 γ = 90
Symmetry Space Group P 1 21 1
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+ VariMax 2012-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.6 50 99 0.113 10.33 3.5 77167 76380 -3 30.271
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 2.6 2.67 99.1 0.393 3.68
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 3R1J 2.6 49.4 76379 3833 98.98 0.2122 0.211 0.2151 0.2345 0.2382 RANDOM 26.9535
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] 1.52 0.52 -1.83 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.11 r_dihedral_angle_3_deg 14.654 r_dihedral_angle_4_deg 13.366 r_dihedral_angle_1_deg 6.06 r_mcangle_it 1.643 r_angle_refined_deg 1.251 r_angle_other_deg 1.095 r_mcbond_it 0.971 r_mcbond_other 0.971 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.11 r_dihedral_angle_3_deg 14.654 r_dihedral_angle_4_deg 13.366 r_dihedral_angle_1_deg 6.06 r_mcangle_it 1.643 r_angle_refined_deg 1.251 r_angle_other_deg 1.095 r_mcbond_it 0.971 r_mcbond_other 0.971 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15795 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 13
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction