6LPU
Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with L-2-hydroxyglutarate (L-2-HG)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL17U1 |
Synchrotron site | SSRF |
Beamline | BL17U1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-05-10 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9792 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 71.709, 94.530, 72.789 |
Unit cell angles | 90.00, 112.25, 90.00 |
Refinement procedure
Resolution | 47.265 - 2.923 |
R-factor | 0.2256 |
Rwork | 0.224 |
R-free | 0.25500 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6lpn |
RMSD bond length | 0.004 |
RMSD bond angle | 0.986 |
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 | 3.110 |
High resolution limit [Å] | 2.923 | 6.460 | 3.000 |
Rmerge | 0.220 | 0.079 | 0.742 |
Rmeas | 0.250 | 0.091 | 0.843 |
Rpim | 0.115 | 0.043 | 0.389 |
Number of reflections | 19104 | 1966 | 1877 |
<I/σ(I)> | 3.9 | ||
Completeness [%] | 99.5 | 99.3 | 97.8 |
Redundancy | 4.8 | 4.7 | 4.4 |
CC(1/2) | 0.989 | 0.651 |
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 |