3UAN
Crystal structure of 3-O-sulfotransferase (3-OST-1) with bound PAP and heptasaccharide substrate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.5 | 293 | Crystals of the 3-OST-1/PAP/heptasaccharide complex were obtained using micro-batch technique, by mixing 1.5 mL of the complex (12.9 mg/mL 3-OST-1, 5 mM heptasaccharide, 4 mM PAP, 23.6 mM Tris pH 7.5, 142 mM NaCl) was mixed with 2.5 mL of 0.1 M sodium citrate pH 5.5 and 20% PEG 3000. Crystals grew to a usable size after 10 days incubation at room temperature. The crystals were transferred in two steps to a cryoprotectant solution containing 0.1 M sodium citrate pH 5.5, 0.1 M NaCl, 4 mM PAP, 20 mM heptasaccharide, 30% PEG3000, and 7.6% ethylene glycol. , temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.883 | α = 90 |
b = 62.168 | β = 95.16 |
c = 86.373 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 93 | IMAGE PLATE | MAR scanner 345 mm plate | 2011-03-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.844 | 25 | 96.95 | 0.05 | 21.8 | 3.7 | 46408 | 44993 | 26.97 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.844 | 1.88 | 84.6 | 0.314 | 3.11 | 2.9 | 2039 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | Rfree | PDB ENTRY 1ZRH | 1.844 | 24.57 | 46408 | 44993 | 2247 | 93.2 | 0.175 | 0.175 | 0.1742 | 0.2023 | random |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
5.5316 | 3.9567 | 0.1457 | -5.6773 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.97 |
f_angle_d | 0.838 |
f_chiral_restr | 0.056 |
f_bond_d | 0.004 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4103 |
Nucleic Acid Atoms | |
Solvent Atoms | 266 |
Heterogen Atoms | 236 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
MOLREP | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |