4Z0P
Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in complex with NADPH and oxalate
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-G |
Synchrotron site | APS |
Beamline | 21-ID-G |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2014-11-06 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 0.97856 |
Spacegroup name | P 32 2 1 |
Unit cell lengths | 108.099, 108.099, 80.226 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 50.000 - 1.700 |
R-factor | 0.1351 |
Rwork | 0.134 |
R-free | 0.14970 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4weq |
RMSD bond length | 0.010 |
RMSD bond angle | 1.475 |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | HKL-3000 |
Refinement software | REFMAC (5.8.0107) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.730 |
High resolution limit [Å] | 1.700 | 4.610 | 1.700 |
Rmerge | 0.074 | 0.033 | 0.852 |
Rmeas | 0.069 | 0.038 | 0.938 |
Rpim | 0.031 | 0.017 | 0.430 |
Total number of observations | 255923 | ||
Number of reflections | 60027 | ||
<I/σ(I)> | 8.3 | 2.4 | |
Completeness [%] | 99.9 | 86.8 | 100 |
Redundancy | 6.9 | 4.6 | 6.7 |
CC(1/2) | 0.999 | 0.726 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 7 | 289 | 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, 5 mM NADPH, and 50 mM oxalic acid pH=7.0 were mixed with 0.2 ul of the MCSG Suite 2 condition #28 (0.2M Ammonium Citrate Tribasic, anhydrous, 20%w/v PEG 3350 pH=7) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop. Before crystallization, the protein-ligand mixture was incubated with 1/15 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours |