8PIE
Crystal structure of the human nucleoside diphosphate kinase B domain in complex with the product AT-8500 formed by catalysis of compound AT-9010
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SOLEIL BEAMLINE PROXIMA 2 |
| Synchrotron site | SOLEIL |
| Beamline | PROXIMA 2 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-04-15 |
| Detector | DECTRIS EIGER X 9M |
| Wavelength(s) | 0.9801073689120102 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 54.190, 120.313, 71.918 |
| Unit cell angles | 90.00, 110.15, 90.00 |
Refinement procedure
| Resolution | 49.680 - 1.900 |
| Rwork | 0.172 |
| R-free | 0.21300 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.014 |
| RMSD bond angle | 2.050 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | REFMAC (5.8.0405) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 49.680 | 1.968 |
| High resolution limit [Å] | 1.900 | 1.900 |
| Rpim | 0.055 | 0.330 |
| Number of reflections | 67263 | 6623 |
| <I/σ(I)> | 8.61 | 2.57 |
| Completeness [%] | 98.9 | 98 |
| Redundancy | 7.1 | 7.2 |
| CC(1/2) | 0.996 | 0.793 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 277 | mixing 1:1 ration with precipitant solution composed of: -50mM Tris-HCl pH8.4 -12% PEG3350 -16% glycerol |
