5TSD
Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH and oxalate
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2015-10-17 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 0.97872 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 68.945, 70.124, 126.615 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.000 - 1.900 |
R-factor | 0.1566 |
Rwork | 0.155 |
R-free | 0.19760 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4xcv |
RMSD bond length | 0.009 |
RMSD bond angle | 1.328 |
Data reduction software | DENZO |
Data scaling software | HKL-3000 |
Phasing software | HKL-3000 |
Refinement software | REFMAC (5.8.0151) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.930 |
High resolution limit [Å] | 1.900 | 5.160 | 1.900 |
Rmerge | 0.077 | 0.027 | 0.863 |
Number of reflections | 49321 | ||
<I/σ(I)> | 6.1 | 1.71 | |
Completeness [%] | 99.9 | 99.7 | 99.9 |
Redundancy | 6.5 | 6.1 | 6.5 |
CC(1/2) | 0.998 | 0.748 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 289 | 0.2 ul of 14.8 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #93 (0.1M Bis-Tris, 25%w/v PEG 3350 pH=5.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/13 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours |