8G9E
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCF2P)-IP5, an analog of 5-IP7
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 22-ID |
| Synchrotron site | APS |
| Beamline | 22-ID |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2020-09-18 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 1 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 88.082, 109.899, 41.090 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 38.520 - 1.750 |
| R-factor | 0.1267 |
| Rwork | 0.124 |
| R-free | 0.17520 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 3t9d |
| RMSD bond length | 0.011 |
| RMSD bond angle | 1.642 |
| Data reduction software | HKL-2000 |
| Data scaling software | HKL-2000 |
| Phasing software | REFMAC |
| Refinement software | REFMAC (5.8.0352) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 50.000 | 50.000 | 1.780 |
| High resolution limit [Å] | 1.750 | 4.750 | 1.750 |
| Rmerge | 0.087 | 0.047 | 0.790 |
| Rmeas | 0.096 | 0.052 | 0.879 |
| Rpim | 0.040 | 0.021 | 0.379 |
| Total number of observations | 220730 | ||
| Number of reflections | 40858 | 2258 | 2030 |
| <I/σ(I)> | 11.3 | ||
| Completeness [%] | 99.1 | 99.6 | 99.5 |
| Redundancy | 5.4 | 5.5 | 5.1 |
| CC(1/2) | 0.994 | 0.673 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 14% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP, 2 mM CdCl2, Soaking with 2mM 5-PCF2P-InsP5 under pH 5.2 for 3 days , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
