5DHU
Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID14-4 |
Synchrotron site | ESRF |
Beamline | ID14-4 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2012-10-06 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 0.978002 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 66.920, 119.340, 67.750 |
Unit cell angles | 90.00, 100.37, 90.00 |
Refinement procedure
Resolution | 47.453 - 2.330 |
R-factor | 0.2255 |
Rwork | 0.225 |
R-free | 0.25900 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2i1w |
RMSD bond length | 0.005 |
RMSD bond angle | 0.533 |
Data reduction software | MOSFLM |
Data scaling software | SCALA (3.3.21) |
Phasing software | PHENIX |
Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 66.643 | 59.670 | 2.460 |
High resolution limit [Å] | 2.330 | 7.370 | 2.330 |
Rmerge | 0.016 | 0.441 | |
Rmeas | 0.046 | ||
Rpim | 0.028 | 0.012 | 0.377 |
Total number of observations | 111019 | 4540 | 18182 |
Number of reflections | 41403 | ||
<I/σ(I)> | 13.1 | 35.2 | 2.1 |
Completeness [%] | 92.6 | 98.8 | 100 |
Redundancy | 2.7 | 3.1 | 2.8 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 291.15 | 30 mM sodium bromide, 220 mM potassium citrate, pH 4.8-5.1, glycerol 6%, 15-16% w/v polyethylene glycol 400 |