2Q41
Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1XJ5 | PDB entry 1XJ5 |
Crystallization
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.46 | 50.09 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 88.814 | α = 90 |
b = 95.207 | β = 104.96 |
c = 89.164 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | Re-refinement using ensemble model | THROUGHOUT | PDB entry 1XJ5 | 2.7 | 26.29 | 37779 | 3788 | 95.5 | 0.164 | 0.164 | 0.249 | RANDOM | 37.2 |
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] | |
-2.91 | 1.24 | 14.18 | -11.27 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.6 |
c_scangle_it | 5.02 |
c_mcangle_it | 3.87 |
c_scbond_it | 3.12 |
c_mcbond_it | 2.19 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.95 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 8864 |
Nucleic Acid Atoms | |
Solvent Atoms | 576 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
CNS | phasing |