4CBQ
Crystal structure of the thioredoxin reductase from Entamoeba histolytica with auranofin Au(I) bound to Cys286
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.5 | 0.2 M LITHIUM SULPHATE, 100 MM TRIS, PH 8.5; 25% PEG 3350, 3 MM AURANOFIN | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.29 | 46.37 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 65.622 | α = 90 |
| b = 91.625 | β = 90 |
| c = 103.682 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 110 | CCD | MARRESEARCH | MIRRORS | 2011-10-29 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 | |
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 | 1.94 | 103.68 | 99.1 | 0.07 | 9.2 | 3.9 | 46526 | 0.5 | 32.8 | ||||||||||
| 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 | 1.94 | 2.04 | 97.1 | 0.7 | 1.6 | 3.8 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4A65 | 1.94 | 68.75 | 44071 | 2340 | 98.76 | 0.17069 | 0.16808 | 0.2185 | RANDOM | 34.943 | ||||||
| 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] | |
| -0.27 | -0.85 | 1.12 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.067 |
| r_dihedral_angle_4_deg | 16.123 |
| r_dihedral_angle_3_deg | 14.175 |
| r_dihedral_angle_1_deg | 6.277 |
| r_scbond_it | 3.826 |
| r_mcangle_it | 3.525 |
| r_mcbond_it | 2.752 |
| r_mcbond_other | 2.746 |
| r_angle_refined_deg | 1.942 |
| r_angle_other_deg | 0.901 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4684 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 417 |
| Heterogen Atoms | 222 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
