3IAU
The structure of the processed form of threonine deaminase isoform 2 from Solanum lycopersicum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 277 | Protein Solution (10 mg/ml protein, 0.05 M NaCl, 0.003 M NaN3, 0.005 M Bis-Tris pH 7) mixed in a 1:1 ratio with the Well Solution (32% Polyethylene glycol 1500, 0.1 M LiSO4, 0.1 M Sodium Acetate pH 4.5). Cryoprotected with 32% Polyethylene glycol 1500, 0.1 M LiSO4, 5% ethylene glycol, 0.1 M Sodium Acetate pH 4.5, vapor diffusion, hanging drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.42 | 72.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 136.834 | α = 90 |
b = 136.834 | β = 90 |
c = 254.226 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | mirrors and beryllium lenses | 2009-04-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.97957 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.35 | 50 | 100 | 0.133 | 7.5 | 21.5 | 58877 | 26.65 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.35 | 2.43 | 100 | 0.676 | 19.9 | 5776 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.353 | 48.559 | 1.34 | 58785 | 2979 | 99.8 | 0.166 | 0.164 | 0.199 | 32.753 |
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] | |
1.684 | 1.684 | -3.368 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.409 |
f_angle_d | 0.914 |
f_chiral_restr | 0.061 |
f_bond_d | 0.005 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5324 |
Nucleic Acid Atoms | |
Solvent Atoms | 654 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |