4QOY
Novel binding motif and new flexibility revealed by structural analysis of a pyruvate dehydrogenase-dihydrolipoyl acetyltransferase sub-complex from the escherichia coli pyruvate dehydrogenase multi-enzyme complex
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 | 6.3 | 298 | 20% PEG3350 0.2M AMMONIUM TARTRATE DIBASIC,SODIUM AZIDE, PH 6.35, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 59.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 210.94 | α = 90 |
b = 326.84 | β = 90 |
c = 77.21 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | MARMOSAIC 225 mm CCD | MIRRORS | 2011-07-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.0 | APS | 22-BM |
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 | 2.8 | 32.29 | 99.7 | 0.136 | 7.1 | 6.32 | 132370 | 132035 | 82.01 |
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 | 2.8 | 2.9 | 99.8 | 0.605 | 1.5 | 4.15 | 13058 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | DIFFERENCE FOURIER | THROUGHOUT | PDB ENTRY 2IEA | 2.8 | 32.29 | 132370 | 124907 | 6292 | 94.36 | 0.1999 | 0.1982 | 0.2328 | RANDOM | 80.53 |
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] | |
-0.9855 | 0.7342 | 0.2514 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_dihedral_angle_d | 15.14 |
t_it | 5.5 |
t_other_torsion | 3.15 |
t_omega_torsion | 2.75 |
t_ideal_dist_contact | 2.089 |
t_angle_deg | 1 |
t_chiral_improper_torsion | 0.079 |
t_gen_planes | 0.014 |
t_bond_d | 0.009 |
t_trig_c_planes | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 27874 |
Nucleic Acid Atoms | |
Solvent Atoms | 1293 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
d*TREK | data reduction |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
SERGUI | data collection |
d*TREK | data scaling |
PHASER | phasing |
BUSTER | refinement |