2G25
E. Coli Pyruvate Dehydrogenase Phosphonolactylthiamin Diphosphate Complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1L8A | PDB ENTRY 1L8A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 291 | PEG2000 MONOMETHYL ETHER, PROPANOL, SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, PHOSPHONOLACTYL- THIAMIN DIPHOSPHATE, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.57 | α = 90 |
b = 142.51 | β = 102.37 |
c = 82.09 | 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 | AREA DETECTOR | SIEMENS HI-STAR | Osmic Mirrors | 2002-03-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
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 | 2.1 | 40.5 | 94 | 0.065 | 0.087 | 24.82 | 4.7 | 99699 | 99699 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
2.1 | 2.19 | 60 | 5.51 |
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-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | DIFFERENCE FOURIER | THROUGHOUT | PDB ENTRY 1L8A | 2.1 | 8 | 2 | 99699 | 95052 | 4807 | 94 | 0.204 | 0.185 | 0.185 | 0.244 | RANDOM | 10.55 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 24.87 |
x_scangle_it | 3.129 |
x_scbond_it | 2.166 |
x_mcangle_it | 1.698 |
x_angle_deg | 1.3 |
x_mcbond_it | 1.11 |
x_improper_angle_d | 0.72 |
x_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13182 |
Nucleic Acid Atoms | |
Solvent Atoms | 564 |
Heterogen Atoms | 95 |
Software
Software | |
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Software Name | Purpose |
X-GEN | data scaling |
FBSCALE | data reduction |
PHASES | phasing |
X-PLOR | refinement |
FRAMBO | data collection |
FBSCALE | data scaling |