5TJL
Crystal structure of GTA + A trisaccharide (mercury derivative)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| 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 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.26 | 45.66 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 52.58 | α = 90 |
| b = 150.66 | β = 90 |
| c = 79.3 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 113 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2009-04-16 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-002 | 1.5418 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
| 1 | 1.89 | 19.92 | 99.3 | 0.047 | 16.3 | 4.74 | 25471 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.89 | 1.96 | 99.9 | 0.317 | 4.4 | 4.56 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1LZ0 | 1.89 | 19.92 | 24171 | 1299 | 99.19 | 0.1897 | 0.1879 | 0.2236 | RANDOM | 31.273 | ||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| -0.26 | 0.78 | -0.52 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.31 |
| r_dihedral_angle_4_deg | 15.739 |
| r_dihedral_angle_3_deg | 11.711 |
| r_dihedral_angle_1_deg | 6.192 |
| r_mcangle_it | 2.08 |
| r_mcbond_it | 1.39 |
| r_mcbond_other | 1.39 |
| r_angle_refined_deg | 1.354 |
| r_angle_other_deg | 0.924 |
| r_chiral_restr | 0.077 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2079 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 86 |
| Heterogen Atoms | 46 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| d*TREK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| d*TREK | data reduction |
| PHASER | phasing |
