9SFO
Crystal structure of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae in complex with ADP and vanadate
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 | 2021-02-11 |
| Detector | DECTRIS PILATUS3 2M |
| Wavelength(s) | 0.87313 |
| Spacegroup name | P 41 21 2 |
| Unit cell lengths | 198.830, 198.830, 72.280 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 70.396 - 3.420 |
| Rwork | 0.204 |
| R-free | 0.26880 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 1.448 |
| Data reduction software | iMOSFLM |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | REFMAC (5.8.0425) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 72.280 | 3.690 |
| High resolution limit [Å] | 3.420 | 3.420 |
| Rmerge | 0.376 | 0.978 |
| Rmeas | 0.412 | 1.068 |
| Rpim | 0.165 | 0.419 |
| Total number of observations | 116947 | 24602 |
| Number of reflections | 20087 | 4041 |
| <I/σ(I)> | 4.5 | 2.2 |
| Completeness [%] | 99.7 | |
| Redundancy | 5.8 | 6.1 |
| CC(1/2) | 0.914 | 0.802 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | 24% PEG 3350, 100 mM MES pH 7.0 |
