Crystal structure of a putative L-allo-threonine aldolase (lmo0305) from Listeria monocytogenes EGD-E at 1.80 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.36 | 277 | 53.80% 2-methyl-2,4-pentanediol, 0.1M TRIS pH 8.36, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.38 | 48.3 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 85.593 | α = 90 |
| b = 96.642 | β = 110.81 |
| c = 99.478 | 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 | CCD | MAR MAR325 | 2010-05-13 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.96109,0.97915,0.97936 | SSRL | BL9-2 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 29.699 | 94.4 | 138522 | -3 | 16.78 | |||||||||||||
| 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 | 1.8 | 1.86 | 95.3 | 0.371 | 1.9 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MAD | 1.8 | 29.7 | 138490 | 6965 | 98.9 | 0.163 | 0.162 | 0.17 | 0.198 | 0.2 | 18.96 | |||||||
| 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] | |
| -0.11 | -0.38 | 0.67 | -0.83 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.227 |
| r_dihedral_angle_4_deg | 13.338 |
| r_dihedral_angle_3_deg | 10.187 |
| r_dihedral_angle_1_deg | 3.458 |
| r_scangle_it | 2.962 |
| r_scbond_it | 1.835 |
| r_angle_refined_deg | 1.488 |
| r_mcangle_it | 1.016 |
| r_angle_other_deg | 0.931 |
| r_mcbond_it | 0.59 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 11243 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1522 |
| Heterogen Atoms | 59 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SOLVE | phasing |
| REFMAC | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| qfit | model building |
| XDS | data reduction |
