2ZE8
Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 277 | 1.4-2.0M sodium formate, 5mM magnesium chloride, 0.1M sodium acetate buffer, 20mM dimethylallyl diphosphate, pH 4.8-5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.51 | α = 90 |
b = 97.568 | β = 90 |
c = 131.108 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 110 | CCD | RIGAKU JUPITER 210 | 2004-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL45PX | 1.0000 | SPring-8 | BL45PX |
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 | 2.8 | 131.31 | 97.83 | 29244 | 39.384 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 2.8 | 131.31 | 29244 | 1566 | 97.83 | 0.23385 | 0.2303 | 0.30218 | RANDOM | 85.639 |
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] | |
3.88 | 4.1 | -7.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.186 |
r_dihedral_angle_4_deg | 24.805 |
r_dihedral_angle_3_deg | 24.088 |
r_dihedral_angle_1_deg | 8.853 |
r_angle_refined_deg | 2.975 |
r_mcangle_it | 1.884 |
r_scangle_it | 1.818 |
r_scbond_it | 1.15 |
r_mcbond_it | 1.148 |
r_nbtor_refined | 0.377 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7260 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |