3R5W
Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3R5R | PDB entry 3R5R (preliminary model) |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277 | 3.6 M Na-formate, 10% glycerol with equimolar protein and F420, pH 8.5, vapor diffusion, sitting drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.8 | 67.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.336 | α = 90 |
b = 89.419 | β = 96.29 |
c = 127.678 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2009-07-10 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2009-07-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 0.979 | ALS | 5.0.2 |
2 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 0.979 | ALS | 5.0.2 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.786 | 50 | 97.5 | 0.073 | 22.9 | 3.1 | 174250 | 174250 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.786 | 1.86 | 96.3 | 0.722 | 1.6 | 3.2 | 17150 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB entry 3R5R (preliminary model) | 1.786 | 42.169 | 0.08 | 159399 | 159341 | 7913 | 88.14 | 0.175 | 0.1733 | 0.2064 | random | 31.0082 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.5771 | -2.9673 | 0.4187 | 0.1584 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 22.058 |
f_angle_d | 1.568 |
f_chiral_restr | 0.103 |
f_bond_d | 0.013 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8740 |
Nucleic Acid Atoms | |
Solvent Atoms | 1280 |
Heterogen Atoms | 530 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
BOS | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |