Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1YDW | PDB entry 1YDW |
Crystallization
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.55 | 51.75 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 58.197 | α = 90 |
| b = 107.663 | β = 90 |
| c = 129.748 | 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 | M | SINGLE WAVELENGTH | ||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | Re-refinement using ensemble model | THROUGHOUT | PDB entry 1YDW | 2.49 | 29.73 | 28857 | 1472 | 98.4 | 0.215 | 0.215 | 0.23 | 0.285 | 0.29 | RANDOM | 31.4 | ||||
| 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] | |
| 0.42 | 3.32 | -3.74 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 23 |
| c_scangle_it | 3.15 |
| c_scbond_it | 2.09 |
| c_mcangle_it | 2.04 |
| c_angle_deg | 1.3 |
| c_mcbond_it | 1.22 |
| c_improper_angle_d | 0.85 |
| c_bond_d | 0.006 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5340 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 123 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| CNS | phasing |
