2Q4D
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 | |
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Matthews coefficient | Solvent content |
2.49 | 50.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.589 | α = 90 |
b = 80.427 | β = 102.97 |
c = 50.709 | γ = 90 |
Symmetry | |
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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 | R-Free | 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 | 0.207 | 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 | |
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Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
CNS | phasing |