2ZE6
Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with substrate analog, DMASPP
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 S-thiolodiphosphate, pH 4.8-5.4., VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.417 | α = 90 |
b = 96.417 | β = 90 |
c = 65.068 | γ = 90 |
Symmetry | |
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Space Group | P 42 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 | 2004-11-18 | 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 | 2.1 | 68.2 | 98.29 | 17222 | 24.01 |
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 | 2.1 | 68.2 | 17222 | 934 | 98.29 | 0.19957 | 0.19633 | 0.26424 | RANDOM | 52.277 |
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] | |
3.08 | 3.08 | -6.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.323 |
r_dihedral_angle_4_deg | 21.642 |
r_dihedral_angle_3_deg | 19.523 |
r_dihedral_angle_1_deg | 7.028 |
r_scangle_it | 5.124 |
r_scbond_it | 3.615 |
r_angle_refined_deg | 2.605 |
r_mcangle_it | 2.112 |
r_mcbond_it | 1.373 |
r_nbtor_refined | 0.317 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1824 |
Nucleic Acid Atoms | |
Solvent Atoms | 38 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |