4OO4
Crystal Structure of Human Thioredoxin Mutant
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1ERT | PDB ENTRY 1ERT |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4 | 289 | 20% PEG 3350, 0.1 M sodium acetate, 2 mM DTT, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.93 | 36.36 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 35.269 | α = 90 |
| b = 50.182 | β = 94.08 |
| c = 51.066 | 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 | PIXEL | PSI PILATUS 6M | RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR | 2011-01-07 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.9796 | SSRL | BL9-2 |
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 | 0.97 | 50.94 | 84.2 | 0.042 | 18.8 | 3.4 | 88291 | 88291 | |||||||||||
| 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 | 0.97 | 1.02 | 44.5 | 0.316 | 2.6 | 1.6 | |||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1ERT | 0.97 | 35.75 | 83851 | 83851 | 4412 | 84.1 | 0.13726 | 0.13582 | 0.16498 | RANDOM | 14.371 | |||||
| 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] | |
| -1.12 | -1.25 | 1.51 | -0.21 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_sphericity_free | 54.765 |
| r_dihedral_angle_2_deg | 32.9 |
| r_sphericity_bonded | 21.469 |
| r_dihedral_angle_3_deg | 14.126 |
| r_long_range_B_refined | 10.597 |
| r_long_range_B_other | 7.011 |
| r_dihedral_angle_1_deg | 6.099 |
| r_rigid_bond_restr | 5.264 |
| r_scangle_other | 2.697 |
| r_scbond_it | 2.51 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1634 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 340 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALA | data scaling |
