3D3S
Crystal structure of L-2,4-diaminobutyric acid acetyltransferase from Bordetella parapertussis
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.3 | 289 | 1.26 M Ammonium sulfate, 0.1 M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K, pH 6.3 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.98 | 37.95 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 69.16 | α = 90 |
| b = 63.145 | β = 96.06 |
| c = 77.331 | 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 | ADSC QUANTUM 315 | Mirrors | 2008-03-22 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97932 | APS | 19-ID |
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 | 1.87 | 48.8 | 99.9 | 0.078 | 12.3 | 4.1 | 55224 | 55224 | 29.14 | ||||||||||
| 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 | 1.87 | 1.9 | 99.5 | 0.669 | 2 | 3.9 | 2729 | ||||||||||||
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-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.87 | 48.8 | 52345 | 52345 | 2802 | 99.46 | 0.167 | 0.167 | 0.165 | 0.21 | RANDOM | 36.15 | |||||
| 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] | |
| -1.58 | -0.23 | 1.85 | -0.32 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.268 |
| r_dihedral_angle_4_deg | 20.204 |
| r_dihedral_angle_3_deg | 17.074 |
| r_dihedral_angle_1_deg | 5.566 |
| r_scangle_it | 4.618 |
| r_scbond_it | 3.056 |
| r_mcangle_it | 2.007 |
| r_angle_refined_deg | 1.757 |
| r_mcbond_it | 1.282 |
| r_nbtor_refined | 0.308 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4818 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 377 |
| Heterogen Atoms | 100 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SBC-Collect | data collection |
| HKL-3000 | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| MLPHARE | phasing |
| DM | phasing |
| SHELXD | phasing |
| RESOLVE | phasing |
| Coot | model building |
