5TJL
Crystal structure of GTA + A trisaccharide (mercury derivative)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU MICROMAX-002 |
Temperature [K] | 113 |
Detector technology | IMAGE PLATE |
Collection date | 2009-04-16 |
Detector | RIGAKU RAXIS IV++ |
Wavelength(s) | 1.5418 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 52.580, 150.660, 79.300 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 19.920 - 1.890 |
R-factor | 0.1897 |
Rwork | 0.188 |
R-free | 0.22360 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1lz0 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.354 |
Data reduction software | d*TREK |
Data scaling software | d*TREK (8.0SSI) |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0155) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 19.920 | 19.920 | 1.960 |
High resolution limit [Å] | 1.890 | 4.060 | 1.890 |
Rmerge | 0.047 | 0.031 | 0.317 |
Number of reflections | 25471 | ||
<I/σ(I)> | 16.3 | 40 | 4.4 |
Completeness [%] | 99.3 | 95.3 | 99.9 |
Redundancy | 4.74 | 4.79 | 4.56 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 277 | The first crystals of GTA/GTB were grown as mercury derivatives (Patenaude, S.I., et al. 2002): 10 ul drops with 6-8 mg/ml protein, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) pH 7.5, 50 mM, sodium acetate pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (v/v) 2-methyl-2,4-pentanediol (MPD), 5%(v/v) glycerol, 2%(w/v) PEG 4000, and 0.3-0.5 mM 3-chloromercuri-2-methoxypropylurea suspended over 1 ml of a resevoir solution: 50 mM ADA pH 7.5, 10 mM MnCl2, 100 mM ammonium sulfate, 5%(v/v) MPD, 10%(v/v) glycerol, and 8-10%(w/v) PEG 4000. Crystals were washed with artificial mother liquor ML-1 consisting of 10% polyethylene glycol (PEG) 4000, 30 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) buffer pH 7.5, 30 mM sodium acetate buffer pH 4.6, 100 mM ammonium sulfate, 10 mM MnCl2 and 30% glycerol as the cryoprotectant. Crystals of GTA/GTB in complex with the A and B trisaccharides were obtained by soaking them in mother liquor ML-1 with 30% glycerol and 45-50 mM substrates for 2-5 days at 18 degrees Celsius |