4J5I

Crystal structure of an alpha-ketoglutarate-dependent taurine dioxygenase from Mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R1JPDB entry 3R1J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289MysmA.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 coefficientSolvent content
2.3848.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.01α = 90
b = 166.68β = 90.57
c = 99.72γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+VariMax2012-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.650990.11310.333.57716776380-330.271
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6799.10.3933.68

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3R1J2.649.476379383398.980.21220.2110.2345RANDOM26.9535
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]
1.520.52-1.830.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.11
r_dihedral_angle_3_deg14.654
r_dihedral_angle_4_deg13.366
r_dihedral_angle_1_deg6.06
r_mcangle_it1.643
r_angle_refined_deg1.251
r_angle_other_deg1.095
r_mcbond_it0.971
r_mcbond_other0.971
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.11
r_dihedral_angle_3_deg14.654
r_dihedral_angle_4_deg13.366
r_dihedral_angle_1_deg6.06
r_mcangle_it1.643
r_angle_refined_deg1.251
r_angle_other_deg1.095
r_mcbond_it0.971
r_mcbond_other0.971
r_chiral_restr0.069
r_bond_refined_d0.009
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15795
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms13

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction