7ZZF
Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a linear di-adenosine derivative
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID23-2 |
Synchrotron site | ESRF |
Beamline | ID23-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-06-11 |
Detector | DECTRIS PILATUS 2M |
Wavelength(s) | 0.873128 |
Spacegroup name | I 2 2 2 |
Unit cell lengths | 63.532, 74.848, 119.339 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 59.670 - 2.410 |
R-factor | 0.196 |
Rwork | 0.194 |
R-free | 0.23070 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6rg9 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHENIX (1.19.1_4122) |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 59.670 | 59.669 | 2.125 |
High resolution limit [Å] | 1.941 | 6.163 | 1.941 |
Rmerge | 0.097 | 0.031 | 1.023 |
Rmeas | 0.111 | 0.036 | 1.143 |
Rpim | 0.053 | 0.017 | 0.501 |
Total number of observations | 2266 | 3345 | |
Number of reflections | 136858 | 648 | 649 |
<I/σ(I)> | 9.8 | 28.1 | 1.6 |
Completeness [%] | 88.5 | 86.7 | 61.6 |
Redundancy | 4.1 | 3.5 | 5.2 |
CC(1/2) | 0.998 | 0.999 | 0.542 |
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 |