2QTA
E. coli Pyruvate dehydrogenase E1 component E401K mutant with thiamin diphosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2IEA | PDB ENTRY 2IEA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.05 | 295 | PEG 2000 monomethyl ether, proponal, sodium azide, hepes buffer, magnesium chloride, thiamin diphosphate, pH 7.05, Vapour diffusion, temperature 295K, VAPOR DIFFUSION, SITTING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.81 | α = 90 |
b = 141.83 | β = 102.01 |
c = 82.56 | 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 | 100 | CCD | MARMOSAIC 300 mm CCD | 2006-03-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.00 | APS | 22-ID |
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 | 38.06 | 98.7 | 0.074 | 0.074 | 27.92 | 6.8 | 155239 | 151931 | 14.4 |
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 | 1.85 | 1.92 | 94.2 | 0.336 | 0.336 | 7.7 | 6 | 14769 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 2IEA | 1.85 | 38.06 | 151931 | 151931 | 7685 | 97.1 | 0.225 | 0.225 | 0.214 | 0.237 | RANDOM | 20.6 |
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] | |
-0.52 | 2.15 | -2.94 | 3.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23 |
c_angle_deg | 1.4 |
c_improper_angle_d | 1.01 |
c_mcangle_it | 0.48 |
c_scangle_it | 0.365 |
c_mcbond_it | 0.257 |
c_scbond_it | 0.21 |
c_bond_d | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12682 |
Nucleic Acid Atoms | |
Solvent Atoms | 413 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |