6LPT
Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-lactate (D-LAC)
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 | 72.263, 94.411, 73.575 |
Unit cell angles | 90.00, 111.77, 90.00 |
Refinement procedure
Resolution | 36.387 - 2.621 |
R-factor | 0.1931 |
Rwork | 0.191 |
R-free | 0.23130 |
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 | 2.710 |
High resolution limit [Å] | 2.620 | 5.640 | 2.620 |
Rmerge | 0.154 | 0.060 | 0.656 |
Rmeas | 0.166 | 0.065 | 0.708 |
Rpim | 0.063 | 0.025 | 0.265 |
Total number of observations | 188447 | ||
Number of reflections | 27511 | 2801 | 2738 |
<I/σ(I)> | 3 | ||
Completeness [%] | 99.5 | 99.1 | 99.9 |
Redundancy | 6.8 | 6.7 | 7 |
CC(1/2) | 0.998 | 0.841 |
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 |