7NNJ
Crystal Structure of NUDT4 (Diphosphoinositol polyphosphate phosphohydrolase 2) in complex with 4-O-Bn-1-PCP-InsP4 (AMR2105)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I03 |
| Synchrotron site | Diamond |
| Beamline | I03 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2018-07-07 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.9763 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 40.181, 40.772, 197.688 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 39.932 - 1.755 |
| R-factor | 0.1976 |
| Rwork | 0.195 |
| R-free | 0.24470 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5tlu |
| RMSD bond length | 0.008 |
| RMSD bond angle | 1.070 |
| Data reduction software | Aimless |
| Data scaling software | Aimless |
| Phasing software | PHASER (2.5.6) |
| Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 98.844 | 98.844 | 1.926 |
| High resolution limit [Å] | 1.755 | 5.541 | 1.755 |
| Rmerge | 0.103 | 0.040 | 2.700 |
| Rmeas | 0.105 | 0.041 | 2.756 |
| Rpim | 0.021 | 0.009 | 0.547 |
| Total number of observations | 617285 | 26322 | 30634 |
| Number of reflections | 24365 | 1218 | 1219 |
| <I/σ(I)> | 21.7 | 70.7 | 1.5 |
| Completeness [%] | 91.5 | 100 | 56.1 |
| Redundancy | 25.3 | 21.6 | 25.1 |
| CC(1/2) | 1.000 | 1.000 | 0.610 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 2.75 M sodium formate |
