2IFQ
Crystal structure of S-nitroso thioredoxin
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 32% PEG 4000, 50 mM sodium phosphate, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.8 | 31.63 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 116.08 | α = 90 |
| b = 25.749 | β = 97.97 |
| c = 85.86 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 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 | ADSC QUANTUM 315 | bent Si-mirror | 2006-04-15 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | APS | 14-BM-C | |
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 | 1.2 | 25.1 | 97.1 | 0.07 | 9.1 | 5.1 | 79717 | 79717 | 16.5 | ||||||||||
| 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) | |||||||||||
| 1.2 | 1.24 | 98.4 | 0.24 | 3.3 | 4.8 | 7774 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | FOURIER SYNTHESIS | THROUGHOUT | PDB entry 2HXK | 1.2 | 25.13 | 73521 | 73521 | 3882 | 97.1 | 0.17859 | 0.17716 | 0.20565 | RANDOM | 13.78 | |||||
| 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] | |
| -0.39 | -0.03 | 0.25 | 0.14 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.516 |
| r_dihedral_angle_3_deg | 14.112 |
| r_sphericity_free | 11.053 |
| r_dihedral_angle_1_deg | 6.275 |
| r_sphericity_bonded | 5.508 |
| r_scangle_it | 5.499 |
| r_scbond_it | 4.278 |
| r_mcangle_it | 3.07 |
| r_rigid_bond_restr | 2.655 |
| r_mcbond_it | 2.548 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2685 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 115 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDISPLAYF | data collection |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
