6S5F
Structure of the human RAB39B in complex with GMPPNP
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I03 |
| Synchrotron site | Diamond |
| Beamline | I03 |
| Temperature [K] | 80 |
| Detector technology | PIXEL |
| Collection date | 2019-05-17 |
| Detector | DECTRIS EIGER2 X 16M |
| Wavelength(s) | 0.91587 |
| Spacegroup name | P 1 2 1 |
| Unit cell lengths | 52.725, 35.285, 53.605 |
| Unit cell angles | 90.00, 107.51, 90.00 |
Refinement procedure
| Resolution | 50.280 - 1.700 |
| R-factor | 0.186 |
| Rwork | 0.184 |
| R-free | 0.22860 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2a5j |
| RMSD bond length | 0.011 |
| RMSD bond angle | 1.584 |
| Data reduction software | DIALS |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER (2.8.2) |
| Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 50.280 | 50.280 | 1.730 |
| High resolution limit [Å] | 1.700 | 9.000 | 1.700 |
| Rmerge | 0.105 | 0.056 | 0.842 |
| Rmeas | 0.115 | 0.060 | 0.923 |
| Rpim | 0.045 | 0.023 | 0.373 |
| Total number of observations | 134548 | ||
| Number of reflections | 20997 | 160 | 1110 |
| <I/σ(I)> | 8.8 | 22.3 | 1.8 |
| Completeness [%] | 99.9 | 99.3 | 99.9 |
| Redundancy | 6.4 | 6.5 | 6 |
| CC(1/2) | 0.997 | 0.997 | 0.843 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.1 | 293 | 0.1 M HEPES pH 7.1, 19 % PEG3350 |
