3HJ8
Crystal structure determination of catechol 1,2-dioxygenase from rhodococcus opacus 1CP in complex with 4-chlorocatechol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3HGI | PDB ENTRY 3HGI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 296 | 39% PEG400, 0.1M Hepes, 0.1M magnesium chloride, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.6 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 89.572 | ¦Á = 90 |
b = 37.501 | ¦Â = 95.03 |
c = 74.917 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 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 | CCD | OXFORD ONYX CCD | 2007-04-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION ENHANCE ULTRA | 1.542 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.37 | 20 | 87.7 | 0.05 | 21.16 | 2.03 | 9161 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.37 | 2.4 | 79.5 | 0.197 | 2.57 | 1.37 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 3HGI | 2.4 | 20 | 8752 | 400 | 88.2 | 0.199 | 0.195 | 0.288 | RANDOM | 34.85 |
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] | |
0.69 | 1.16 | 0.81 | -1.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.411 |
r_dihedral_angle_4_deg | 25.169 |
r_dihedral_angle_3_deg | 15.856 |
r_dihedral_angle_1_deg | 5.907 |
r_scangle_it | 2.067 |
r_scbond_it | 1.277 |
r_angle_refined_deg | 1.275 |
r_mcangle_it | 0.954 |
r_mcbond_it | 0.521 |
r_nbtor_refined | 0.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1991 |
Nucleic Acid Atoms | |
Solvent Atoms | 156 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
CrysalisPro | data collection |
REFMAC | refinement |
CrysalisPro | data reduction |
CrysalisPro | data scaling |