8T92
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-D-(1,2,3,4)-IP4
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 | 2021-12-16 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 1.0 |
| Spacegroup name | C 2 2 21 |
| Unit cell lengths | 62.532, 104.128, 103.862 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 37.330 - 2.300 |
| R-factor | 0.17142 |
| Rwork | 0.168 |
| R-free | 0.22845 |
| Structure solution method | FOURIER SYNTHESIS |
| RMSD bond length | 0.012 |
| RMSD bond angle | 1.851 |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | PHASER |
| Refinement software | REFMAC (5.8.0253) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 50.000 | 50.000 | 2.340 |
| High resolution limit [Å] | 2.300 | 6.240 | 2.300 |
| Rmerge | 0.138 | 0.104 | 0.903 |
| Rmeas | 0.143 | 0.108 | 0.933 |
| Rpim | 0.034 | 0.027 | 0.224 |
| Total number of observations | 299894 | ||
| Number of reflections | 15183 | 826 | 750 |
| <I/σ(I)> | 8.4 | ||
| Completeness [%] | 99.2 | 97.8 | 99.2 |
| Redundancy | 19.8 | 18.4 | 15.6 |
| CC(1/2) | 0.978 | 0.982 | 0.873 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 12% PEG8000, 100mM HEPES pH 7.0, 10mM NaH2PO4, 10% Ethylene Glycol, 5mM ADP and 10mM MgCl2, then soaked in 25% PEG8000, 100mM HEPES pH 7.0, 20% Ethylene Glycol with 5mM D-scyllo- (1,2,3,4)IP4, 5mM ADP and 10mM MgCl2 |
