2GN1
Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 2.2A resolution (Triclinic form with one dimer of TdcB in the asymmetric unit)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GN0 | BIODEGRADATIVE THREONINE DEAMINASE FROM SALMONELLA TYPHIMURIUM (PDB CODE 1GN0) |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 0.1 M citrate buffer pH 6.0, 20% PEG 3350 and 10% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.317 | α = 103.09 |
b = 55.3 | β = 94.7 |
c = 67.235 | γ = 112.94 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MAR scanner 345 mm plate | Osmic mirror | 2005-12-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.542 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.2 | 30 | 94.7 | 0.053 | 22.18 | 12.19 | 29556 | 31.42 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1 | 2.2 | 2.28 | 84.5 | 0.222 | 4.98 | 2494 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | BIODEGRADATIVE THREONINE DEAMINASE FROM SALMONELLA TYPHIMURIUM (PDB CODE 1GN0) | 2.2 | 25 | 26557 | 26557 | 1405 | 94.32 | 0.21183 | 0.20964 | 0.25291 | RANDOM | 32.816 |
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] | |
1.76 | 2.34 | 0.94 | 2.5 | 0.92 | -1.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.666 |
r_dihedral_angle_3_deg | 12.703 |
r_dihedral_angle_4_deg | 12.482 |
r_dihedral_angle_1_deg | 5.47 |
r_scangle_it | 1.538 |
r_angle_refined_deg | 1.025 |
r_scbond_it | 0.885 |
r_angle_other_deg | 0.741 |
r_mcangle_it | 0.563 |
r_mcbond_it | 0.312 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4789 |
Nucleic Acid Atoms | |
Solvent Atoms | 274 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |