6LPN
Crystal structure of human D-2-hydroxyglutarate dehydrogenase in apo form
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 | 2018-10-22 |
| Detector | PSI PILATUS 6M |
| Wavelength(s) | 0.9789 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 72.258, 94.859, 72.740 |
| Unit cell angles | 90.00, 113.34, 90.00 |
Refinement procedure
| Resolution | 39.834 - 2.206 |
| R-factor | 0.1697 |
| Rwork | 0.167 |
| R-free | 0.21690 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 3pm9 |
| RMSD bond length | 0.006 |
| RMSD bond angle | 1.062 |
| 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 | 2.280 |
| High resolution limit [Å] | 2.200 | 4.740 | 2.200 |
| Rmerge | 0.269 | 0.172 | 0.897 |
| Rmeas | 0.292 | 0.188 | 0.988 |
| Rpim | 0.112 | 0.073 | 0.407 |
| Total number of observations | 299485 | ||
| Number of reflections | 45047 | 4562 | 4468 |
| <I/σ(I)> | 2.8 | ||
| Completeness [%] | 99.7 | 99.1 | 99.9 |
| Redundancy | 6.6 | 6.6 | 5.6 |
| CC(1/2) | 0.972 | 0.609 |
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 |
