3OBZ
Crystal structure of human phytanoyl-COA dioxygenase phyhd1 2-oxoglutarate and iron complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 296 | 7%(v/v) PEG 3350, 0.2M calcium acetate and 0.2M KCl Crystals were grown in anaerobic environment and soaked with FeSO4 and 2-oxoglutarate to form complex, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.366 | α = 90 |
b = 92.366 | β = 90 |
c = 81.754 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 TITAN CCD | multilayer | 2007-04-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION SUPERNOVA | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.15 | 24.307 | 99.8 | 0.067 | 0.067 | 17.8 | 3.2 | 22253 | 22253 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
2.15 | 2.27 | 99.7 | 0.371 | 0.371 | 0.448 | 0.248 | 2 | 3.1 | 3181 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | In-house SAD structure | 2.15 | 24.307 | 22230 | 1081 | 99.7 | 0.2328 | 0.2744 | RANDOM | 36.0944 |
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] | |
-2.258 | -0.809 | -2.258 | 4.516 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 3.225 |
c_mcangle_it | 2.203 |
c_scbond_it | 2.091 |
c_mcbond_it | 1.326 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2278 |
Nucleic Acid Atoms | |
Solvent Atoms | 189 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
CNS | refinement |
PDB_EXTRACT | data extraction |
CrysalisPro | data collection |
CrysalisPro | data reduction |