Structure of IDP01002, a putative oxidoreductase from and essential gene of Salmonella typhimurium
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1ZSX | PDB code 1ZSX was used for MR on a crystal diffracting to 2.15 A on our RAXIS4 home source. The protein atoms from the model refined from that crystal were used for rigid body refinement with the new data diffracting to 1.55 A. |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | EVAPORATION | 6.5 | 295 | crystallized in 0.2 M Calcium Acetate, 9% PEG8000 and 0.1 M Sodium Cacodylate. Cryoprotected with 25% ethylene glycol., pH 6.5, EVAPORATION, temperature 295K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.05 | 59.69 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 127.096 | α = 90 |
| b = 127.096 | β = 90 |
| c = 120.492 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 4 |
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 | mirrors | 2008-02-02 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
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 | 1.55 | 30 | 97.2 | 0.06 | 23.08 | 5.2 | 136598 | 132754 | 17.8 | ||||||||||
| 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 | 1.55 | 1.61 | 80.3 | 0.477 | 2.62 | 4.6 | 13638 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB code 1ZSX was used for MR on a crystal diffracting to 2.15 A on our RAXIS4 home source. The protein atoms from the model refined from that crystal were used for rigid body refinement with the new data diffracting to 1.55 A. | 1.55 | 29.96 | 125986 | 6743 | 96.83 | 0.15465 | 0.15342 | 0.15 | 0.17771 | 0.18 | RANDOM. R-free set for the second crystal was imported from the first crystal and extended to 1.55 A | 23.404 | ||||
| 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] | |
| -1.03 | -1.03 | 2.05 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.256 |
| r_dihedral_angle_4_deg | 14.284 |
| r_dihedral_angle_3_deg | 11.137 |
| r_scangle_it | 5.191 |
| r_dihedral_angle_1_deg | 4.478 |
| r_scbond_it | 3.316 |
| r_mcangle_it | 2.137 |
| r_angle_refined_deg | 1.517 |
| r_mcbond_it | 1.309 |
| r_chiral_restr | 0.12 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4920 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 844 |
| Heterogen Atoms | 71 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |














