6Z61
Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE MASSIF-1 |
Synchrotron site | ESRF |
Beamline | MASSIF-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-07-16 |
Detector | DECTRIS PILATUS3 2M |
Wavelength(s) | 0.966 |
Spacegroup name | I 2 2 2 |
Unit cell lengths | 62.585, 75.423, 118.131 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 59.070 - 2.470 |
R-factor | 0.2222 |
Rwork | 0.220 |
R-free | 0.27930 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6rg9 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHENIX |
Refinement software | PHENIX (1.17.1_3660) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 59.070 | 59.065 | 2.372 |
High resolution limit [Å] | 2.241 | 6.794 | 2.241 |
Rmerge | 0.060 | 0.035 | 0.694 |
Rmeas | 0.063 | 0.037 | 0.821 |
Rpim | 0.019 | 0.012 | 0.423 |
Total number of observations | 6046 | 1959 | |
Number of reflections | 11262 | 561 | 563 |
<I/σ(I)> | 22.1 | 62.8 | 1.5 |
Completeness [%] | 89.0 | 100 | 43.2 |
Redundancy | 9.9 | 10.8 | 3.5 |
CC(1/2) | 0.999 | 0.999 | 0.700 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 291.15 | 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400 |