1MY6
The 1.6 A Structure of Fe-Superoxide Dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus : Correlation of EPR and Structural Characteristics
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ISC | FeSOD from E.coli, PDB entry 1isc |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.7 | 293.15 | VAPOR DIFFUSION, HANGING DROP, 293.15K, 0.1M Sodium Cacodylate pH 6.7, 0.2M Magnesium Acetate Tetrahydrate, 20% PEG 6K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.749 | α = 90 |
b = 63.644 | β = 110.45 |
c = 74.709 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | ADSC QUANTUM 4 | 2002-06-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X8C | 1.100 | NSLS | X8C |
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 | 1.6 | 70 | 94.5 | 0.088 | 6.35 | 16.18 | 53851 | -3 | 15.3 |
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) | ||||||||||
1.6 | 1.642 | 93.4 | 0.32 | 0.32 | 6.35 | 14.28 | 5643 |
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 | FeSOD from E.coli, PDB entry 1isc | 1.6 | 70 | 53851 | 2896 | 94.46 | 0.19577 | 0.19377 | 0.23208 | RANDOM | 15.669 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
1.64 | 0.82 | -1.54 | 0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.88 |
r_scangle_it | 3.693 |
r_sphericity_free | 3.671 |
r_scbond_it | 2.616 |
r_sphericity_bonded | 2.124 |
r_mcangle_it | 1.91 |
r_angle_refined_deg | 1.623 |
r_rigid_bond_restr | 1.522 |
r_mcbond_it | 1.312 |
r_angle_other_deg | 0.903 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3128 |
Nucleic Acid Atoms | |
Solvent Atoms | 565 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
EPMR | phasing |