3T9E
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP, 5-(PP)-IP5 (5-IP7) and MgF3 (transition state mimic)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 22-BM |
| Synchrotron site | APS |
| Beamline | 22-BM |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2011-03-11 |
| Detector | MARMOSAIC 225 mm CCD |
| Wavelength(s) | 1.0 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 89.070, 109.987, 41.338 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 37.500 - 1.900 |
| R-factor | 0.17495 |
| Rwork | 0.173 |
| R-free | 0.21263 |
| Structure solution method | FOURIER SYNTHESIS |
| RMSD bond length | 0.011 |
| RMSD bond angle | 1.312 |
| Data reduction software | HKL-2000 |
| Data scaling software | HKL-2000 |
| Phasing software | PHENIX |
| Refinement software | REFMAC (5.5.0110) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 1.930 |
| High resolution limit [Å] | 1.900 | 1.900 |
| Number of reflections | 32911 | |
| <I/σ(I)> | 19.6 | 3.2 |
| Completeness [%] | 99.8 | 99.4 |
| Redundancy | 5.8 | 4.8 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 277 | 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP, 2 mM CdCl2, Soaking with 2mM 5-IP7 and 10 mM NaF under pH 5.2 for 2 days , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
