Crystal Structure of a Putative Succinate-Semialdehyde Dehydrogenase from Salmonella typhimurium LT2 with bound NAD
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 4.6 | 298 | 2M Na Formate, 0.1M Na Acetate pH4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.19 | 61.42 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 133.826 | α = 90 |
| b = 133.826 | β = 90 |
| c = 245.276 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 2 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 | MARMOSAIC 300 mm CCD | BE LENES | 2008-02-04 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | APS | 21-ID-G | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 50 | 100 | 0.09 | 8.5 | 11.6 | 189522 | -3 | |||||||||||
| 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 | 1.9 | 1.97 | 100 | 0.422 | 5.73 | 11.7 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.9 | 50 | 189522 | 10062 | 99.9 | 0.16 | 0.159 | 0.1678 | 0.185 | 0.1913 | RANDOM | 21.83 | |||||
| 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] | |
| -0.22 | -0.11 | -0.22 | 0.32 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.946 |
| r_dihedral_angle_4_deg | 18.108 |
| r_dihedral_angle_3_deg | 12.213 |
| r_dihedral_angle_1_deg | 5.8 |
| r_scangle_it | 4.071 |
| r_scbond_it | 2.646 |
| r_angle_refined_deg | 1.352 |
| r_mcangle_it | 1.325 |
| r_mcbond_it | 1.009 |
| r_nbtor_refined | 0.3 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 13615 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 2320 |
| Heterogen Atoms | 176 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| BLU-MAX | data collection |
| SHELXD | phasing |
| SHARP | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
