8S3D
Crystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 2-amino-2-hydroxyglutarate (reaction intermediate) and NAD
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P13 (MX1) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-06-21 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.9762 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 111.832, 155.707, 163.089 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 65.890 - 1.650 |
R-factor | 0.1471 |
Rwork | 0.147 |
R-free | 0.17350 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.012 |
RMSD bond angle | 1.153 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.18.1_3865) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 65.890 | 1.750 |
High resolution limit [Å] | 1.650 | 1.650 |
Rmerge | 0.092 | 1.445 |
Rmeas | 1.548 | |
Number of reflections | 337626 | 53784 |
<I/σ(I)> | 6.83 | 1.11 |
Completeness [%] | 99.5 | 98.7 |
Redundancy | 7.49 | 7.56 |
CC(1/2) | 0.994 | 0.532 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.1M Amino acids (0.02M DL-Glutamic acid monohydrate; 0.02M DL-Alanine; 0.02M Glycine; 0.02M DL-Lysine monohydrochloride; 0.02M DL-Serine ) 0.1M Imidazole/MES monohydrate pH 6.5 20% v/v PEG 500* MME; 10 % w/v PEG 20000 |