4JZ2
Crystal structure of Co ion substituted SOD2 from Clostridium difficile
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 | 7.8 | 289 | 0.2M sodium citrate dihydrogen, 20% PEG 3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.81 | 74.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.321 | α = 90 |
b = 80.321 | β = 90 |
c = 250.991 | 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 | |||||
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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 | 1.95 | 50 | 98.8 | 0.143 | 0.144 | 17.8 | 8.9 | 34420 | 1 | 1 | 33 |
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 | 1.95 | 1.98 | 100 | 0.657 | 0.692 | 3.2 | 9 |
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 (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 | 1.95 | 40.706 | 1 | 1 | 34420 | 1719 | 95.03 | 0.217 | 0.1824 | 0.182 | 0.1904 | RANDOM | 33 |
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] | |
-3.3009 | -3.3009 | 6.6018 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.441 |
f_angle_d | 0.978 |
f_chiral_restr | 0.076 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1669 |
Nucleic Acid Atoms | |
Solvent Atoms | 154 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASES | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |