5X9U
Crystal structure of group III chaperonin in the open state
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | MICROBATCH | 295 | 3 mM ADP, 200 mM NH4Cl, 10mM MgCl2, 50mM HEPES sodium (pH 7.0), 5% w/v Polyethylene glycol PEG 8000, 3% 1,8-Diaminooctane | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.12 | 70.14 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 209.78 | α = 90 |
| b = 209.78 | β = 90 |
| c = 169.813 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 4 21 2 |
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 | DECTRIS PILATUS 2M | 2015-05-23 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 1.10000 | Photon Factory | BL-1A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 4 | 50 | 99.7 | 8.4 | 20.3 | 32570 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5X9V,3KFE | 4.001 | 49.446 | 1.33 | 32468 | 1647 | 99.65 | 0.2563 | 0.2529 | 0.321 | |||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 15.115 |
| f_angle_d | 1.029 |
| f_chiral_restr | 0.038 |
| f_bond_d | 0.005 |
| f_plane_restr | 0.004 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 14665 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 108 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| XDS | data processing |
| Coot | model building |
