2Q4A
Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g21360
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1Y0Z | PDB entry 1Y0Z |
Crystallization
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 145.276 | α = 90 |
b = 61.094 | β = 121.68 |
c = 114.681 | 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 1Y0Z | 2.39 | 43.63 | 32733 | 1628 | 96.8 | 0.171 | 0.171 | 0.235 | RANDOM | 30.4 |
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] | |
2.58 | 5.31 | -0.08 | -2.51 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.2 |
c_scangle_it | 4.02 |
c_mcangle_it | 3.23 |
c_scbond_it | 2.59 |
c_mcbond_it | 1.89 |
c_angle_deg | 1.5 |
c_improper_angle_d | 1.09 |
c_bond_d | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5141 |
Nucleic Acid Atoms | |
Solvent Atoms | 780 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
CNS | phasing |