3EF6
Crystal structure of Toluene 2,3-Dioxygenase Reductase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1D7Y | pdb entry: 1D7Y including all side chains |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.7 | 286 | 0.1 M Tris pH 8.5, 1.5 M (NH)4SO 2 and 12% (v/v) glycerol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 286K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.128 | α = 90 |
b = 77.128 | β = 90 |
c = 156.372 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | CCD | ADSC QUANTUM 210 | 2004-02-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 1.0332 | NSLS | X6A |
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 | 1.8 | 19.86 | 99 | 0.076 | 9.24 | 44352 | 1 | 1 |
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 | 1.8 | 1.86 | 96.4 | 0.386 | 4 | 7.04 | 4216 |
Refinement
Statistics | |||||||||||||||||||
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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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry: 1D7Y including all side chains | 1.8 | 20 | 44198 | 44198 | 2229 | 99.28 | 0.205 | 0.205 | 0.203 | 0.243 | RANDOM | 28.002 |
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] | |
1.09 | 1.09 | -2.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.31 |
r_dihedral_angle_4_deg | 17.776 |
r_dihedral_angle_3_deg | 13.779 |
r_dihedral_angle_1_deg | 5.622 |
r_scangle_it | 3.389 |
r_scbond_it | 2.071 |
r_angle_refined_deg | 1.521 |
r_mcangle_it | 1.299 |
r_mcbond_it | 0.86 |
r_nbtor_refined | 0.297 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2940 |
Nucleic Acid Atoms | |
Solvent Atoms | 465 |
Heterogen Atoms | 105 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
d*TREK | data reduction |