4QGN
Human acireductone dioxygenase with iron ion and L-methionine in active center
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 277 | Protein: 20 mg/ml in 50 mM Tris-HCl pH 7.8, 150mM NaCl, 2.5mM L-selenomethionine, Crystallization condition: 0.1M sodium acetate, ammonium sulfate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.99 | 58.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.195 | α = 90 |
b = 105.195 | β = 90 |
c = 40.822 | γ = 120 |
Symmetry | |
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Space Group | P 64 |
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 315 | Rosenbaum-Rock vertical focusing mirror, with Pt, glass, Pd lanes | 2012-06-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97912 | APS | 19-ID |
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 | 3.05 | 50 | 99.8 | 0.182 | 0.182 | 11.037 | 6.1 | 5073 | 5073 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.05 | 3.1 | 100 | 0.726 | 0.726 | 2.118 | 4.9 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1vr3 | 3.05 | 37.25 | 4829 | 4829 | 232 | 99.72 | 0.17994 | 0.17753 | 0.2279 | RANDOM | 33.363 |
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] | |
-3.22 | -1.61 | -3.22 | 4.84 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.544 |
r_dihedral_angle_3_deg | 16.611 |
r_dihedral_angle_4_deg | 14.445 |
r_dihedral_angle_1_deg | 6.629 |
r_angle_refined_deg | 1.276 |
r_angle_other_deg | 0.836 |
r_chiral_restr | 0.064 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1487 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
Coot | model building |
HKL-3000 | phasing |
CCP4 | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |