3I9U
Crystal structure of the rat heme oxygenase (HO-1) in complex with heme binding dithioerythritol (DTE)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3I9T | PDB ENTRY 3I9T |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.4 | 293 | 3.2M sodium formate, 10mM sodium azide, 5mM DTV, pH7.4, VAPOR DIFFUSION, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.53 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 65.882 | ¦Á = 90 |
b = 65.882 | ¦Â = 90 |
c = 120.244 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 32 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 | 95 | CCD | ADSC QUANTUM 4r | 2006-02-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-6A | 1 | Photon Factory | BL-6A |
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 | 2.25 | 50 | 99.9 | 0.062 | 32.1 | 7.2 | 14964 | 30.585 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.25 | 2.33 | 99.9 | 0.329 | 7.04 | 7.3 | 1454 |
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 3I9T | 2.25 | 30 | 14140 | 754 | 99.98 | 0.16961 | 0.16683 | 0.22266 | RANDOM | 29.132 |
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] | |
1.76 | 0.88 | 1.76 | -2.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.719 |
r_dihedral_angle_3_deg | 16.255 |
r_dihedral_angle_4_deg | 15.26 |
r_dihedral_angle_1_deg | 5.673 |
r_scangle_it | 5.026 |
r_scbond_it | 3.17 |
r_angle_refined_deg | 1.913 |
r_mcangle_it | 1.912 |
r_mcbond_it | 1.06 |
r_chiral_restr | 0.129 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1711 |
Nucleic Acid Atoms | |
Solvent Atoms | 101 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |