3R5P

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R5LPDB entry 3R5L (preliminary model used for MR)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42771.6M (NH4)2SO4, 0.1M Citric acid, pH 4.0, vapor diffusion, sitting drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3763.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.176α = 90
b = 96.176β = 90
c = 33.704γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-04-17SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.976ALS5.0.3

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
11.855097.90.11312.45.11521515215
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)
11.851.9281.60.5721.2143.61238

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 3R5L (preliminary model used for MR)1.8541.6450.16143561435072292.360.17270.17110.2027random24.6311
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]
3.17523.1752-6.3505
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.227
f_angle_d1.747
f_chiral_restr0.136
f_bond_d0.018
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms905
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms10

Software

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