2AHU
Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from Escherichia coli O157:H7.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | 294 | 22.5 % (w/v) PEG 4000, 3% (v/v) isopropanol and 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.129 | α = 90 |
b = 133.308 | β = 100.57 |
c = 105.838 | 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 | ADSC QUANTUM 4 | mirrors | 2004-06-12 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | mirrors | 2004-06-12 | M | MAD | |||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X8C | 1.1 | NSLS | X8C |
2 | SYNCHROTRON | NSLS BEAMLINE X8C | 0.9799, 0.9795, 0.9646 | NSLS | X8C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.9 | 50 | 94.3 | 0.053 | 20.1 | 3 | 491266 | 163843 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1,2 | 1.9 | 1.97 | 71.8 | 0.284 | 4.4 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.9 | 50 | 163804 | 148789 | 15015 | 94.34 | 0.19026 | 0.18714 | 0.22044 | RANDOM | 27.689 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.78 | 0.27 | -0.65 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.572 |
r_dihedral_angle_4_deg | 15.175 |
r_dihedral_angle_3_deg | 14.498 |
r_dihedral_angle_1_deg | 5.321 |
r_scangle_it | 2.759 |
r_scbond_it | 1.808 |
r_angle_refined_deg | 1.143 |
r_mcangle_it | 1.048 |
r_mcbond_it | 0.697 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15696 |
Nucleic Acid Atoms | |
Solvent Atoms | 1271 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |