3B96
Structural Basis for Substrate Fatty-Acyl Chain Specificity: Crystal Structure of Human Very-Long-Chain Acyl-CoA Dehydrogenase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 0.1 M HEPES, 17.6% PEG 2000, 0.047 M MgCl2, 5% glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.616 | α = 90 |
b = 107.879 | β = 90 |
c = 149.776 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2006-05-14 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | 2006-05-14 | M | SINGLE WAVELENGTH | |||||||
3 | 1 | x-ray | 100 | CCD | 2006-05-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | 1.5419 | |||
2 | SYNCHROTRON | APS BEAMLINE 19-ID | 1.0083 | APS | 19-ID |
3 | SYNCHROTRON | APS BEAMLINE 5ID-B | 1.1405 | APS | 5ID-B |
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 | ||||||||
1,2,3 | 1.91 | 50 | 98.8 | 0.079 | 15.2 | 7.6 | 46776 |
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) | |||||||||||
1.91 | 1.98 | 98.4 | 0.532 | 6.7 | 4630 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MIRAS | THROUGHOUT | 1.91 | 30.69 | 46738 | 2371 | 98.65 | 0.162 | 0.159 | 0.216 | RANDOM | 24.049 |
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] | |
0.1 | -0.06 | -0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.3 |
r_dihedral_angle_4_deg | 14.36 |
r_dihedral_angle_3_deg | 14.295 |
r_scangle_it | 9.717 |
r_scbond_it | 7.019 |
r_dihedral_angle_1_deg | 6.034 |
r_mcangle_it | 4.221 |
r_mcbond_it | 3.728 |
r_angle_refined_deg | 1.353 |
r_nbtor_refined | 0.309 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4225 |
Nucleic Acid Atoms | |
Solvent Atoms | 441 |
Heterogen Atoms | 76 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |