3BLX
Yeast Isocitrate Dehydrogenase (Apo Form)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 295 | 16% polyethylene glycol 3350, 0.13 M potassium sulfate, 0.2 M trimethylamine-N-oxide, 15% propanediol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.94 | 58.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 112.444 | α = 111.03 |
b = 115.208 | β = 96.08 |
c = 159.247 | γ = 107.13 |
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 | 2006-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.1000 | NSLS | X29A |
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 | 2.7 | 50 | 96.6 | 0.078 | 13.7 | 3.6 | 185029 | 71.3 |
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) | |||||||||||
2.7 | 2.8 | 94.1 | 0.554 | 2 | 3.7 | 18017 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3BLV | 2.7 | 35.739 | 183432 | 9219 | 96.48 | 0.2407 | 0.2394 | 0.2643 | random | 58.2 |
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] | |
33.2784 | -0.6078 | 1.0639 | 37.3134 | -2.0874 | 18.834 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_angle_deg | 1.275 |
f_bond_d | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 41336 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |