3PKX

Crystal Structure of Toxoflavin Lyase (TflA) bound to Mn(II) and Toxoflavin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.12951.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS (pH 10.5), 0.2M Li2SO4, vapor diffusion, hanging drop, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.448.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.195α = 90
b = 111.195β = 90
c = 57.067γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702010-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.9177CHESSF1

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
11.55099.60.05321.96.641996
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)
1.51.551000.5315.94231

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD1.527.7990.138786189391.940.20690.20570.2301Random26.9205
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]
-7.762-7.76215.524
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.47
f_angle_d1.032
f_chiral_restr0.068
f_bond_d0.006
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1718
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms15

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing