7BY9
Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Nicotinamide Adenine Dinucleotide (NAD)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL26B1 |
Synchrotron site | SPring-8 |
Beamline | BL26B1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-10-14 |
Detector | DECTRIS EIGER X 4M |
Wavelength(s) | 1.0 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 63.156, 83.239, 119.477 |
Unit cell angles | 90.00, 93.42, 90.00 |
Refinement procedure
Resolution | 39.393 - 2.200 |
Rwork | 0.224 |
R-free | 0.28480 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7by8 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.694 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.260 |
High resolution limit [Å] | 2.200 | 2.200 |
Rmerge | 0.198 | 0.535 |
Number of reflections | 62899 | 4635 |
<I/σ(I)> | 4 | 1.6 |
Completeness [%] | 99.0 | |
Redundancy | 4.6 | |
CC(1/2) | 0.966 | 0.913 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | The crystal of wild-type gs-MDH prepared in 0.1 M HEPES (pH 7.5), 10 % polyethylene glycol (PEG) 6000 and 5 % 2-Methyl-2,4-pentanediol (MPD) was soaked into the cryo-protectant containing 2 mM OAA and 2 mM NAD+. |