3R5L

Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP627730% PEG 6000, 1M LiCl, 0.1 M MES, pH 6.0, vapor diffusion, sitting drop, temperature 277K
2VAPOR DIFFUSION, SITTING DROP627730% PEG 6000, 0.1 M MES, pH 6.0, vapor diffusion, sitting drop, temperature 277K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.167α = 90
b = 71.045β = 90
c = 50.528γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-04-04SINGLE WAVELENGTH
22x-ray100CCDADSC QUANTUM 315r2009-04-04SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.979ALS5.0.2
2SYNCHROTRONALS BEAMLINE 5.0.20.979ALS5.0.2

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
1,21.555097.70.09827.53.91746617466
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)
1,21.551.6199.50.6262.53.31735

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD1.5535.5230.03166401662486692.660.18150.17990.2113random24.6062
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]
5.3241-4.0708-1.2532
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.837
f_angle_d1.734
f_chiral_restr0.126
f_bond_d0.015
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms921
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms12

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling