24XI
Crystal structure of the diaminopimelate dehydrogenase from Pyrococcus sp. in its holo form
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | ROTATING ANODE |
| Source details | RIGAKU |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2025-09-30 |
| Detector | RIGAKU HyPix-6000HE |
| Wavelength(s) | 1.54184 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 81.886, 165.904, 82.873 |
| Unit cell angles | 90.00, 107.72, 90.00 |
Refinement procedure
| Resolution | 22.080 - 1.900 |
| R-factor | 0.19963 |
| Rwork | 0.198 |
| R-free | 0.22893 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.012 |
| RMSD bond angle | 1.686 |
| Data reduction software | CrysalisPro |
| Data scaling software | Aimless |
| Phasing software | MOLREP |
| Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 22.080 | 1.930 |
| High resolution limit [Å] | 1.900 | 1.900 |
| Rmerge | 0.113 | 0.496 |
| Rmeas | 0.124 | 0.561 |
| Rpim | 0.052 | 0.256 |
| Total number of observations | 34116 | |
| Number of reflections | 162933 | 7646 |
| <I/σ(I)> | 10.8 | 2.7 |
| Completeness [%] | 98.7 | |
| Redundancy | 5.5 | 4.5 |
| CC(1/2) | 0.995 | 0.789 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 277 | 0.2M Ammonium acetate, 0.1M HEPES pH 7.5, 45% v/v (+/-)-2-Methyl-2,4-pentanedio |
