2H73
Crystal Structure of Thioredoxin Mutant D43E in Hexagonal (p61) Space Group
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | COUNTER-DIFFUSION | 7 | 277 | 60% (v/v) MPD, Ac2Cu 1 mM, Hepes 15 mM pH 7.0, Counter-diffusion, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.67 | 54.03 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 102.991 | α = 90 |
| b = 102.991 | β = 90 |
| c = 42.445 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 61 |
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 | BRUKER SMART 6000 | Montel Optics | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | OTHER | 1.5418 | ||
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 | 2.45 | 44.6 | 99.9 | 0.0319 | 22.19 | 9.43 | 9672 | 9672 | 49.495 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.45 | 2.5 | 100 | 0.2322 | 3.93 | 8.26 | 574 | ||||||||||||
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | Throuhgout | pdb entry 2TRX | 2.45 | 44.6 | 9672 | 9589 | 462 | 99.275 | 0.212 | 0.212 | 0.2088 | 0.278 | Random | 28.1 | ||||
| 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] | |
| -3.366 | -1.683 | -3.366 | 5.049 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 41.677 |
| r_dihedral_angle_4_deg | 20.675 |
| r_dihedral_angle_3_deg | 16.752 |
| r_dihedral_angle_1_deg | 6.14 |
| r_scangle_it | 1.976 |
| r_mcangle_it | 1.929 |
| r_angle_refined_deg | 1.731 |
| r_scbond_it | 1.415 |
| r_mcbond_it | 1.265 |
| r_nbtor_refined | 0.313 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1645 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 79 |
| Heterogen Atoms | 16 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SAINT | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| PROTEUM PLUS | data reduction |
| SADABS | data scaling |
| XPREP | data reduction |
| Coot | model building |
| MolProbity | model building |
