4JYY
Crystal structure of the azide and iron substituted Clostrium difficile SOD2 complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3TJT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 289 | 60% (v/v) tacsimateTM, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.81 | 74.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.375 | α = 90 |
b = 80.375 | β = 90 |
c = 250.532 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
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 | mirrors | 2012-01-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.9795 | SSRF | BL17U |
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 | 2.1 | 40.2 | 99.9 | 0.083 | 0.094 | 69.6 | 41.9 | 28940 | 1 | 3 | 35 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.1 | 2.14 | 100 | 0.703 | 0.671 | 9 | 43.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 3TJT | 2.101 | 40.187 | 1 | 1 | 28940 | 28331 | 1962 | 97.78 | 0.219 | 0.1831 | 0.182 | 0.1977 | RANDOM | 35 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.1415 | -1.1415 | 2.2831 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.114 |
f_angle_d | 0.976 |
f_chiral_restr | 0.072 |
f_bond_d | 0.007 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1669 |
Nucleic Acid Atoms | |
Solvent Atoms | 135 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASES | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |