2H6X
Crystal Structure of Thioredoxin Wild Type in Hexagonal (p61) Space Group
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2TRX | PDB entry 2TRX |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | COUNTER-DIFFUSION | 3.5 | 277 | 60% (v/v) MPD, Ac2Cu 1mM, AcNa 15mM, HEPES 15 mM pH 6.9, pH 3.5, Counterdiffusion, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.79 | 55.95 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 102.727 | ¦Á = 90 |
| b = 102.727 | ¦Â = 90 |
| c = 42.865 | ¦Ã = 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 | 2006-03-28 | 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 | 2.6 | 51.36 | 99.8 | 0.0787 | 9.08 | 7.28 | 8147 | 8147 | 51.288 | ||||||||||
| 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 | 2.6 | 2.65 | 100 | 0.3161 | 2.63 | 7.28 | 464 | ||||||||||||
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 | THROUGHOUT | PDB entry 2TRX | 2.6 | 44.5 | 8147 | 8077 | 370 | 99.18 | 0.222 | 0.222 | 0.219 | 0.284 | RANDOM | 43.014 | ||||
| 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] | |
| -0.48 | -0.24 | -0.48 | 0.72 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.224 |
| r_dihedral_angle_3_deg | 16.628 |
| r_dihedral_angle_4_deg | 15.798 |
| r_dihedral_angle_1_deg | 6.349 |
| r_mcangle_it | 1.954 |
| r_scangle_it | 1.636 |
| r_angle_refined_deg | 1.427 |
| r_mcbond_it | 1.193 |
| r_scbond_it | 1.142 |
| r_symmetry_hbond_refined | 0.366 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1636 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 83 |
| Heterogen Atoms | 16 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| PROTEUM PLUS | data reduction |
| SAINT | data scaling |
| SADABS | data scaling |
| XPREP | data reduction |
| AMoRE | phasing |
| Coot | model building |
| MolProbity | model building |
