5V7N
Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADP and 2-Keto-D-gluconic acid
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 | 2016-11-11 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 0.97872 |
Spacegroup name | H 3 |
Unit cell lengths | 175.902, 175.902, 135.336 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 45.110 - 1.750 |
R-factor | 0.1451 |
Rwork | 0.144 |
R-free | 0.16660 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5j23 |
RMSD bond length | 0.011 |
RMSD bond angle | 1.502 |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0158) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.780 |
High resolution limit [Å] | 1.750 | 4.750 | 1.750 |
Rmerge | 0.113 | 0.073 | 0.878 |
Rmeas | 0.129 | 0.084 | 0.987 |
Rpim | 0.060 | 0.041 | 0.447 |
Number of reflections | 156897 | 7876 | |
<I/σ(I)> | 8.6 | 1.8 | |
Completeness [%] | 99.6 | 97.3 | 100 |
Redundancy | 4.9 | 4.3 | 4.9 |
CC(1/2) | 0.990 | 0.607 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.9 | 289 | 0.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADP, 100 mM 2-keto-D-gluconic acid hemicalcium salt + 0.2 uL TOP96 condition #24 (0.2 M magnesium formate, pH 5.9, 20% w/v PEG3350), equilibrated against 1.5 M sodium chloride in a 96-well, 3-drop crystallization plate (Swissci), incubated with 1/20 v/v 1 mg/mL rTEV at 289 K for 3 hours prior to crystallization |