3R5W
Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALS BEAMLINE 5.0.2 |
Synchrotron site | ALS |
Beamline | 5.0.2 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2009-07-10 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 0.979 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 85.336, 89.419, 127.678 |
Unit cell angles | 90.00, 96.29, 90.00 |
Refinement procedure
Resolution | 42.169 - 1.786 |
R-factor | 0.175 |
Rwork | 0.173 |
R-free | 0.20640 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3R5R (preliminary model) |
RMSD bond length | 0.013 |
RMSD bond angle | 1.568 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | PHASER (2.1.4) |
Refinement software | PHENIX (1.5_2) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.860 |
High resolution limit [Å] | 1.786 | 3.880 | 1.786 |
Rmerge | 0.073 | 0.040 | 0.722 |
Number of reflections | 174250 | ||
<I/σ(I)> | 22.9 | 45.667 | 1.6 |
Completeness [%] | 97.5 | 97.1 | 96.3 |
Redundancy | 3.1 | 2.8 | 3.2 |
Crystallization Conditions
crystal 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 |
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 |