7B4P
A Bacteroidetes bacterium CuZn-superoxide dismutase with CuZn metalation
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7B4O |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 295 | .12 M alcohol mix containing 1,6-hexanediol, 1-butanol 1,2-propanediol, 2-propanol, 4-butanediol, 1,3-propanediol; 0.1 M buffer mix containing sodium 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 3-(N-morpholino)propane sulfonic acid pH 7.5; 37.5 % precipitant mix containing 2-Methyl-2,4-pentanediol, polyethylene glycol 1000, polyethylene glycol 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.79 | α = 90 |
b = 109.593 | β = 90 |
c = 122.598 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 16M | 2020-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.9786 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.7 | 81.71 | 100 | 0.999 | 10.6 | 9.2 | 16195 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.7 | 2.83 | 0.61 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7B4O | 2.7 | 81.7 | 16146 | 803 | 99.963 | 0.242 | 0.2396 | 0.2783 | 89.467 |
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] | |
0.931 | 2.595 | -3.526 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.359 |
r_dihedral_angle_3_deg | 12.751 |
r_dihedral_angle_4_deg | 6.934 |
r_dihedral_angle_1_deg | 5.934 |
r_lrange_it | 3.668 |
r_lrange_other | 3.667 |
r_angle_refined_deg | 1.213 |
r_angle_other_deg | 1.067 |
r_mcangle_it | 0.81 |
r_mcangle_other | 0.81 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4427 |
Nucleic Acid Atoms | |
Solvent Atoms | 21 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data reduction |
Aimless | data scaling |
MOLREP | phasing |