8S3B
Crystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 3-(1H-Tetrazol-5-yl)benzoic acid and NAD
This is a non-PDB format compatible entry.
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 | 2021-09-08 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.9763 |
Spacegroup name | P 1 |
Unit cell lengths | 99.809, 109.861, 156.366 |
Unit cell angles | 79.00, 78.48, 72.22 |
Refinement procedure
Resolution | 65.690 - 2.300 |
R-factor | 0.1686 |
Rwork | 0.169 |
R-free | 0.18800 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.008 |
RMSD bond angle | 0.976 |
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] | 75.860 | 2.400 |
High resolution limit [Å] | 2.300 | 2.300 |
Rmerge | 0.073 | 0.430 |
Rmeas | 0.103 | |
Rpim | 0.430 | |
Number of reflections | 230242 | 11515 |
<I/σ(I)> | 8.7 | 2.1 |
Completeness [%] | 91.0 | 62.5 |
Redundancy | 1.99 | 1.93 |
CC(1/2) | 0.997 | 0.720 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 292 | 60mM Divalents (MgCl2, CaCl2) 0.1M Tris (base)/;Bicine pH 8.5 20% v/v PEG 500* MME; 10 % w/v PEG 20000, 10% etylene glycol |