7TN4
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 3-diphosphoinositol 1,2,4,5-tetrakisphosphate (3-PP-IP4), Mg and Fluoride ion
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 | 2021-02-26 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 1.0 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 45.149, 59.743, 62.769 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 31.400 - 1.850 |
| R-factor | 0.1841 |
| Rwork | 0.182 |
| R-free | 0.21730 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 6wo7 |
| RMSD bond length | 0.015 |
| RMSD bond angle | 1.936 |
| Data reduction software | xia2 |
| Data scaling software | SCALEPACK |
| Phasing software | PHASER |
| Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 50.000 | 50.000 | 1.880 |
| High resolution limit [Å] | 1.850 | 5.020 | 1.850 |
| Rmerge | 0.116 | 0.105 | 0.380 |
| Rmeas | 0.122 | 0.110 | 0.399 |
| Rpim | 0.036 | 0.033 | 0.122 |
| Total number of observations | 165071 | ||
| Number of reflections | 14853 | 836 | 726 |
| <I/σ(I)> | 8.4 | ||
| Completeness [%] | 99.5 | 99.5 | 98.4 |
| Redundancy | 11.1 | 11.7 | 9.9 |
| CC(1/2) | 0.987 | 0.982 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | 10% w/v PEG8000, 10% v/v isopropanol, 200 mM lithium sulfate, 100 mM sodium acetate, pH 5.0, 5 mM IP6, soaked in 200 mM lithium chloride, 20% w/v PEG8000, 20% v/v isopropanol, 100 mM sodium acetate, pH 5.0, 20 mM magnesium chloride, 100 mM sodium fluoride in presence of ZmITPK1 reaction solution with 1,2,3,4,5-IP5 |
