1LK9
The Three-dimensional Structure of Alliinase from Garlic
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 293 | PROTEIN: 5 MG/ML ALLIINASE, 5 MM HEPES PH 7.4, 10 % (V/V) GLYCEROL, 0.25 MM PYRIDOXAL-5'-PHOSPHATE, 1 MM S-ETHYL-L-CYSTEINE; PRECIPITANT: 2.9 M AMMONIUM SULFATE, 50 MM HEPES PH 7.4 HANGING DROP METHOD(4 MICROL + 4 MICROL), VAPOUR DIFFUSION, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.49 | 50.6 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 68.45 | ¦Á = 90 |
| b = 101.07 | ¦Â = 90 |
| c = 155.69 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | MARRESEARCH | 2000-04-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | 0.8423 | EMBL/DESY, HAMBURG | BW7B |
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 | 1.53 | 12 | 98.9 | 0.055 | 20.3 | 5.8 | 160747 | 160747 | -3 | 20.7 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.53 | 1.56 | 99.9 | 0.508 | 2.1 | 3.7 | 8024 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | SIRAS | THROUGHOUT | 1.53 | 12 | 162892 | 162892 | 3264 | 98.7 | 0.1929 | 0.2207 | RANDOM | 25.8 | |||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| p_transverse_tor | 25.9 |
| p_staggered_tor | 13.4 |
| p_scangle_it | 4.603 |
| p_planar_tor | 3.9 |
| p_scbond_it | 3.366 |
| p_mcangle_it | 1.364 |
| p_mcbond_it | 0.941 |
| p_multtor_nbd | 0.19 |
| p_singtor_nbd | 0.174 |
| p_xyhbond_nbd | 0.125 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6862 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 830 |
| Heterogen Atoms | 252 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| TRUNCATE | data reduction |
| MLPHARE | phasing |
| REFMAC | refinement |
| CCP4 | data scaling |
