6G50
The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus as isolated.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5F30 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 290 | PRECIPITANT SOLUTION: 0.2 M lithium sulfate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v PEG 3350. Protein solution: TcDH 10 mg/ml 25 mM borate, pH 9.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 56.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.63 | α = 90 |
b = 162.28 | β = 119.51 |
c = 90.57 | 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 | PIXEL | DECTRIS PILATUS3 6M | 2016-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.98400 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 1.65 | 45.4 | 97.3 | 0.098 | 0.996 | 9.2 | 2.6 | 691361 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.65 | 1.7 | 96.8 | 0.79 | 0.51 | 1.65 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 5F30 | 1.65 | 45.31 | 238854 | 26618 | 97.3 | 0.14699 | 0.14261 | 0.20716 | RANDOM | 19.444 |
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] | |
-4.43 | -0.36 | 8.37 | -3.95 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.268 |
r_dihedral_angle_4_deg | 20.494 |
r_dihedral_angle_3_deg | 14.413 |
r_sphericity_free | 12.756 |
r_sphericity_bonded | 10.831 |
r_dihedral_angle_1_deg | 7.862 |
r_long_range_B_refined | 4.121 |
r_scbond_it | 1.982 |
r_mcangle_it | 1.939 |
r_angle_refined_deg | 1.901 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14572 |
Nucleic Acid Atoms | |
Solvent Atoms | 1531 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
Coot | model building |
MOLREP | phasing |