9DKP
The structure of human vacuolar protein sorting 34 catalytic domain bound to RD-I-53
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SSRL BEAMLINE BL12-2 |
| Synchrotron site | SSRL |
| Beamline | BL12-2 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-12-19 |
| Detector | DECTRIS EIGER2 XE 16M |
| Wavelength(s) | 0.979460 |
| Spacegroup name | P 41 21 2 |
| Unit cell lengths | 113.506, 113.506, 145.235 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 53.850 - 2.160 |
| R-factor | 0.2082 |
| Rwork | 0.207 |
| R-free | 0.23530 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.606 |
| Data reduction software | autoPROC |
| Data scaling software | autoPROC |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 53.850 | 2.237 |
| High resolution limit [Å] | 2.160 | 2.160 |
| Rmerge | 0.116 | 3.425 |
| Rmeas | 0.118 | 3.486 |
| Rpim | 0.022 | 0.650 |
| Number of reflections | 51494 | 5068 |
| <I/σ(I)> | 13.99 | 0.99 |
| Completeness [%] | 100.0 | 99.98 |
| Redundancy | 27.5 | 28.5 |
| CC(1/2) | 1.000 | 0.480 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION | 6 | 298 | 20% PEG, 0.2M MES pH 6.0 |
