6LPQ
Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-malate (D-MAL)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SSRF BEAMLINE BL19U1 |
| Synchrotron site | SSRF |
| Beamline | BL19U1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2019-04-29 |
| Detector | PSI PILATUS 6M |
| Wavelength(s) | 0.9788 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 72.615, 94.569, 73.673 |
| Unit cell angles | 90.00, 111.55, 90.00 |
Refinement procedure
| Resolution | 41.136 - 2.800 |
| R-factor | 0.2167 |
| Rwork | 0.215 |
| R-free | 0.25490 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 6lpn |
| RMSD bond length | 0.003 |
| RMSD bond angle | 0.844 |
| Data reduction software | HKL-3000 |
| Data scaling software | HKL-3000 |
| Phasing software | PHENIX |
| Refinement software | PHENIX (1.15rc1_3420) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 50.000 | 50.000 | 2.900 |
| High resolution limit [Å] | 2.800 | 6.030 | 2.800 |
| Rmerge | 0.297 | 0.112 | 0.801 |
| Rmeas | 0.326 | 0.122 | 0.892 |
| Rpim | 0.132 | 0.046 | 0.383 |
| Total number of observations | 132903 | ||
| Number of reflections | 21823 | 2329 | 1878 |
| <I/σ(I)> | 2.2 | ||
| Completeness [%] | 95.7 | 99.7 | 81.8 |
| Redundancy | 6.1 | 6.7 | 5.1 |
| CC(1/2) | 0.994 | 0.617 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 289 | 0.1M BIS-TRIS, pH 6.5, 25% (w/v) PEG 3350 |
