6VBS
The C2 Crystal form of SodCI Superoxide Dismutase at 1.7 A resolution with 6 molecules in the asymmetric unit.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 300 | 20 mg/ml SODC1 plus 1.2 mM trachaeal cytotoxin in 20 mM Tris pH 6.6 150 mM NaCl set up as hanging drop with mother liquor Bis-Tris 0.05M, Ammonium Sulfate 0.05M, 30% Pentaerythritol ethoxylate (15/4 EO/OH) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 42.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 152.838 | α = 90 |
b = 69.474 | β = 116.888 |
c = 95.288 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 100 | PIXEL | DECTRIS EIGER X 9M | 2019-05-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.07812 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.528 | 84.987 | 79.5 | 0.062 | 0.067 | 0.026 | 0.998 | 14.4 | 6.6 | 187907 | 19.48 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.528 | 1.639 | 21 | 0.598 | 0.671 | 0.297 | 0.768 | 1.7 | 4.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6D52 | 1.7 | 35.88 | 1.39 | 187907 | 3497 | 97.69 | 0.1792 | 0.1785 | 0.2189 | 24.1 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 5.7949 |
f_angle_d | 1.0306 |
f_chiral_restr | 0.0538 |
f_bond_d | 0.008 |
f_plane_restr | 0.0069 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6816 |
Nucleic Acid Atoms | |
Solvent Atoms | 849 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
autoPROC | data processing |
XDS | data reduction |
STARANISO | data scaling |
PHENIX | phasing |
PHENIX | refinement |