2Q3T
Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g22680
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VK5 | PDB entry 1VK5 |
Crystallization
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.38 | 63.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.45 | α = 90 |
b = 83.45 | β = 90 |
c = 60.575 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | 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 1VK5 | 1.6 | 31.03 | 32203 | 1633 | 99.9 | 0.139 | 0.139 | 0.17 | RANDOM | 19.2 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.5 |
c_angle_deg | 7.2 |
c_improper_angle_d | 5.33 |
c_scangle_it | 3.31 |
c_scbond_it | 2.27 |
c_mcangle_it | 2.23 |
c_mcbond_it | 1.36 |
c_bond_d | 0.125 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1003 |
Nucleic Acid Atoms | |
Solvent Atoms | 172 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
CNS | phasing |