3T9C
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and inositol hexakisphosphate (IP6)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU MICROMAX-007 HF |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2011-03-05 |
Detector | RIGAKU SATURN 92 |
Wavelength(s) | 1.5418 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 89.037, 110.489, 41.339 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 23.550 - 1.900 |
R-factor | 0.18719 |
Rwork | 0.185 |
R-free | 0.21707 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 3t54 |
RMSD bond length | 0.011 |
RMSD bond angle | 1.335 |
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 | 32957 | |
<I/σ(I)> | 26.1 | 3.1 |
Completeness [%] | 99.7 | 77.4 |
Redundancy | 6.1 | 3.2 |
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 AMPPNP, 2 mM CdCl2, Soaking with 10mM IP6 and 10 mM NaF under pH 5.2 for 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K |