3BJK
Crystal structure of HI0827, a hexameric broad specificity acyl-coenzyme A thioesterase: The Asp44Ala mutant enzyme
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | Reservoir: 30% Saturated sodium citrate, 100 mM Hepes pH 7.5, 5% Ethylene glycol. Protein solution: 16 mg/mL protein in 10 mM Hepes pH 7.5, 150 mM KCl. Hanging drops: 1:1 reservoir and protein solutions. Cryoprotection: increasing ethylene glycol concentration to 18% under perfluoropolyether oil coat, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.56 | 51.99 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 78.487 | α = 90 |
| b = 63.108 | β = 100.14 |
| c = 104.718 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | Osmic mirrors | 2003-05-12 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.9 | 30 | 98 | 0.065 | 8.2 | 6.1 | 79693 | 79693 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1YLI | 1.9 | 29.88 | 78077 | 78077 | 6353 | 99.94 | 0.172 | 0.172 | 0.169 | 0.21 | RANDOM | 31.365 | ||||
| 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] | |
| -0.12 | -0.57 | 0.78 | -0.86 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.139 |
| r_dihedral_angle_4_deg | 16.755 |
| r_dihedral_angle_3_deg | 15.746 |
| r_dihedral_angle_1_deg | 6.183 |
| r_scangle_it | 3.697 |
| r_scbond_it | 2.424 |
| r_angle_refined_deg | 1.662 |
| r_mcangle_it | 1.54 |
| r_mcbond_it | 1.106 |
| r_angle_other_deg | 0.839 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6366 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 463 |
| Heterogen Atoms | 139 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CrystalClear | data collection |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
| CNS | phasing |
