Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1YDH | PDB entry 1YDH |
Crystallization
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.49 | 50.63 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 121.589 | α = 90 |
| b = 80.427 | β = 102.97 |
| c = 50.709 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | APS-1 | 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 1YDH | 2.152 | 34.35 | 25678 | 1300 | 99 | 0.152 | 0.152 | 0.17 | 0.207 | 0.22 | RANDOM | 26.5 | ||||
| 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] | |
| 1.08 | 1.17 | -1.07 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 21.3 |
| c_scangle_it | 2.57 |
| c_scbond_it | 1.96 |
| c_mcangle_it | 1.73 |
| c_mcbond_it | 1.2 |
| c_angle_deg | 1.1 |
| c_improper_angle_d | 0.83 |
| c_bond_d | 0.006 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2796 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 319 |
| Heterogen Atoms | 20 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| CNS | phasing |
