2BMQ
The Crystal Structure of Nitrobenzene Dioxygenase in complex with nitrobenzene
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BMO | PDB ENTRY 2BMO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.1M HEPES PH 6.5, 6% PEG 8000 (W/V), 5MM NISO4, 50 MM NITROBENZENE. THE NITROBENZENE WAS PREPARED FROM A 1M STOCKSOLUTION WHERE NITROBENZENE WAS DISOLVED IN ETHANOL. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.533 | α = 90 |
b = 121.533 | β = 90 |
c = 84.179 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | MARRESEARCH | 2003-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I711 | MAX II | I711 |
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 | 1.55 | 27.63 | 98.5 | 0.08 | 6.7 | 5.1 | 99964 | 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 | 1.55 | 1.63 | 99.7 | 0.51 | 1.4 | 4.3 |
Refinement
Statistics | |||||||||||||||||||
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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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2BMO | 1.55 | 27 | 95726 | 5050 | 98.5 | 0.169 | 0.167 | 0.192 | RANDOM | 17.71 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.44 | -0.22 | -0.44 | 0.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.413 |
r_dihedral_angle_4_deg | 17.613 |
r_dihedral_angle_3_deg | 12.073 |
r_dihedral_angle_1_deg | 6.234 |
r_scangle_it | 2.55 |
r_scbond_it | 1.779 |
r_angle_refined_deg | 1.306 |
r_mcangle_it | 1.095 |
r_mcbond_it | 0.658 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5048 |
Nucleic Acid Atoms | |
Solvent Atoms | 699 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |