3QHP
Crystal structure of the catalytic domain of cholesterol-alpha-glucosyltransferase from Helicobacter pylori
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 297 | 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350, 0.1M glycine, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.786 | α = 101.44 |
b = 40.714 | β = 94.87 |
c = 53.738 | γ = 90.58 |
Symmetry | |
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Space Group | P 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 | 100 | CCD | ADSC QUANTUM 315 | 2008-11-23 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2008-11-28 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0000 | Photon Factory | BL-5A |
2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 0.9194, 0.9196, 0.9062 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | |||||||||
1,2 | 1.5 | 20 | 96 | 45557 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1,2 | 1.5 | 1.53 | 94.3 | 0.141 | 0.138 | 8.6 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.5 | 19.94 | 43082 | 2306 | 95.95 | 0.19757 | 0.196 | 0.22734 | RANDOM | 17.49 |
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] | |
0.1 | 0.12 | -0.27 | -0.11 | -0.62 | -0.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.658 |
r_dihedral_angle_4_deg | 16.81 |
r_dihedral_angle_3_deg | 12.615 |
r_dihedral_angle_1_deg | 6.577 |
r_scangle_it | 3.408 |
r_scbond_it | 2.012 |
r_mcangle_it | 1.413 |
r_angle_refined_deg | 1.315 |
r_mcbond_it | 0.766 |
r_chiral_restr | 0.086 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2440 |
Nucleic Acid Atoms | |
Solvent Atoms | 280 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SOLVE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |