6G21
Crystal structure of an esterase from Aspergillus oryzae
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | ammonium sulphate, Tris buffer |
| 2 | VAPOR DIFFUSION, SITTING DROP | 293 | lithium sulphate, tris buffer,CRYSTALS SOAKED IN 5mM KPTCL4 | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 119.472 | α = 90 |
| b = 119.472 | β = 90 |
| c = 142.85 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2012-05-28 | M | SINGLE WAVELENGTH | ||||||
| 2 | 2 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2012-10-21 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.920 | Diamond | I04-1 |
| 2 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 1.072 | Diamond | I04 |
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 | 2.1 | 37.72 | 100 | 0.099 | 25.6 | 18.5 | 67326 | 24.8 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.1 | 2.15 | 100 | 0.74 | 0.78 | 0.25 | 0.93 | 4.8 | 19.2 | ||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | SIRAS | THROUGHOUT | 2.1 | 37.72 | 64050 | 3246 | 99.98 | 0.15584 | 0.15385 | 0.19429 | RANDOM | 30.347 | |||||||
| 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] | |
| 0.26 | 0.13 | 0.26 | -0.84 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.368 |
| r_dihedral_angle_4_deg | 23.671 |
| r_dihedral_angle_3_deg | 14.281 |
| r_dihedral_angle_1_deg | 6.695 |
| r_long_range_B_refined | 5.287 |
| r_long_range_B_other | 5.263 |
| r_scangle_other | 4.323 |
| r_mcangle_it | 3.083 |
| r_mcangle_other | 3.083 |
| r_scbond_it | 3.014 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7777 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 436 |
| Heterogen Atoms | 213 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| CRANK | phasing |
