6LPP
Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-2-hydroxyglutarate (D-2-HG)
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 | 2019-03-31 |
Detector | PSI PILATUS 6M |
Wavelength(s) | 0.9789 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 72.275, 94.593, 73.399 |
Unit cell angles | 90.00, 111.90, 90.00 |
Refinement procedure
Resolution | 40.781 - 2.650 |
R-factor | 0.2055 |
Rwork | 0.203 |
R-free | 0.24590 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6lpn |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | PHENIX |
Refinement software | PHENIX (1.14_3260) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.740 |
High resolution limit [Å] | 2.639 | 5.710 | 2.650 |
Rmerge | 0.104 | 0.050 | 0.375 |
Rmeas | 0.123 | 0.059 | 0.451 |
Rpim | 0.065 | 0.032 | 0.247 |
Number of reflections | 26662 | 2717 | 2622 |
<I/σ(I)> | 4 | ||
Completeness [%] | 99.0 | 98.7 | 98.1 |
Redundancy | 3.4 | 3.4 | 3.2 |
CC(1/2) | 0.996 | 0.852 |
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 |