1XG3
Crystal structure of the C123S 2-methylisocitrate lyase mutant from Escherichia coli in complex with the reaction product, Mg(II)-pyruvate and succinate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 30% PEG3350, 0.1M (NH)2SO4, 0.1M MES (pH6.0). 5mM Mg(II), 5mM isocitrate, followed by overnight soaking of a crystal in 35% PEG3350, 100 mM succinate, 100 mM pyruvate, 5mM Mg(II), VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 159.358 | α = 90 |
b = 85.993 | β = 108.28 |
c = 99.597 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IV | focusing mirrors (MSC/Yale) | 2004-01-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 1.5418 |
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 | 1.9 | 25.85 | 88.5 | 0.025 | 20.3 | 2.82 | 100609 | 89039 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.9 | 1.97 | 67.5 | 0.084 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | throught | structure of the C123S mutant enzyme in complex with isocitrate | 1.9 | 25.85 | 2 | 100579 | 88761 | 3579 | 88.3 | 0.161 | 0.195 | random |
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] | |
-0.89 | -0.89 | -0.684 | 1.574 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_angle_deg | 1.3 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8702 |
Nucleic Acid Atoms | |
Solvent Atoms | 1049 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | refinement |
CNS | phasing |