6Z65
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 | 2018-11-29 |
Detector | DECTRIS PILATUS3 2M |
Wavelength(s) | 0.966 |
Spacegroup name | I 2 2 2 |
Unit cell lengths | 63.019, 74.531, 118.739 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.120 - 1.970 |
R-factor | 0.2036 |
Rwork | 0.202 |
R-free | 0.22820 |
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] | 48.122 | 48.122 | 1.644 |
High resolution limit [Å] | 1.488 | 5.200 | 1.488 |
Rmerge | 0.036 | 0.016 | 0.626 |
Rmeas | 0.043 | 0.019 | 0.748 |
Rpim | 0.023 | 0.010 | 0.405 |
Total number of observations | 77946 | 4112 | 3734 |
Number of reflections | 17839 | 1162 | 1163 |
<I/σ(I)> | 15.2 | 42.7 | 1.8 |
Completeness [%] | 81.3 | 97.4 | 70.7 |
Redundancy | 3.4 | 3.5 | 3.2 |
CC(1/2) | 0.999 | 1.000 | 0.595 |
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 |