2IEA
E. coli pyruvate dehydrogenase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.05 | 295 | PEG2000 MONOMETHYL ETHER, PROPANOL, SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, THIAMIN DIPHOSPHATE, pH 7.05, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.35 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.69 | α = 90 |
b = 141.6 | β = 102.4 |
c = 82.46 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 93 | CCD | BRANDEIS - B4 | TOROIDAL MIRROR | 2000-01-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12C | NSLS | X12C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.85 | 30 | 92.1 | 0.054 | 0.054 | 17.9 | 3.6 | 149133 | 146183 | 2 | 1 | 11.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.85 | 1.94 | 70.2 | 0.175 | 0.175 | 3.9 | 2.23 | 8471 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.85 | 8 | 1 | 2 | 149133 | 133768 | 8130 | 87 | 0.19 | 0.177 | 0.177 | 0.203 | RANDOM | 19.9 |
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] | |
-0.09 | 1.76 | -0.6 | 0.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.1 |
c_scangle_it | 4.812 |
c_scbond_it | 3.644 |
c_mcangle_it | 2.751 |
c_mcbond_it | 2.222 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.75 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12682 |
Nucleic Acid Atoms | |
Solvent Atoms | 682 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
PHASES | phasing |
CNS | refinement |
MAR345 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |