8PYW
Crystal structure of the human Nucleoside-diphosphate kinase B domain bound to compound diphosphate form of AT-9052-Sp.
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 | 2022-12-10 |
| Detector | DECTRIS EIGER X 9M |
| Wavelength(s) | 0.980105 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 54.220, 121.060, 70.760 |
| Unit cell angles | 90.00, 107.14, 90.00 |
Refinement procedure
| Resolution | 48.668 - 1.553 |
| Rwork | 0.170 |
| R-free | 0.19950 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.011 |
| RMSD bond angle | 1.738 |
| Data reduction software | XDS (Jan 10, 2022 ; BUILT=20220110) |
| Data scaling software | XSCALE (Jan 10, 2022 ; BUILT=20220820) |
| Phasing software | PHASER (VERSION 2.8.3) |
| Refinement software | REFMAC (5.8.0419) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 48.668 | 1.580 |
| High resolution limit [Å] | 1.553 | 1.553 |
| Rpim | 0.037 | 0.321 |
| Number of reflections | 121746 | 5881 |
| <I/σ(I)> | 11.4 | 2.1 |
| Completeness [%] | 97.2 | 93.9 |
| Redundancy | 3.9 | 3.2 |
| CC(1/2) | 0.997 | 0.723 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 277 | co-crystallisation with diphosphate AT-9052F compound. |
