1PD2
CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEX WITH GLUTATHIONE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION METHOD RESERVOIR SOLUTION: 18% (W/V) PEG 6K, 100 MM AMMONIUM CITRATE 5MM CACL2, 10MM DTT, 2% (V/V) 1,4-DIOXANE PROTEIN SOLUTION: 7.3 MG/ML PROTEIN (50 MM TRIS-HCL [PH 7.5]) EACH 4 UL WAS MIXED FOR DROPLET |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 46.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.5 | α = 90 |
b = 56.5 | β = 90 |
c = 233.4 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 | 298 | IMAGE PLATE | RIGAKU | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-6A | Photon Factory | BL-6A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.3 | 40 | 95.1 | 0.085 | 4 | 77899 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MIRAS | PROCHECK | 2.3 | 6 | 2 | 17811 | 95.1 | 0.204 | 0.289 | RANDOM |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_angle_deg | 1.613 |
x_bond_d | 0.01 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na | |
x_angle_deg_prot | |
x_dihedral_angle_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3296 |
Nucleic Acid Atoms | |
Solvent Atoms | 99 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
WEIS | data scaling |
ROTAVATA | data reduction |
PHASES | phasing |
X-PLOR | refinement |
WEIS | data reduction |
CCP4 | data scaling |
ROTAVATA | data scaling |