3SO7
Organophoshatedegrading enzyme (OpdA)-phosphate complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291 | 0.4 M sodium potassium tartrate tetrahydrate pH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 59.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.189 | α = 90 |
b = 109.189 | β = 90 |
c = 62.932 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | Cu FINE FOCUS | 1.54 |
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 | 2.2 | 94.56 | 100 | 0.105 | 0.105 | 8.3 | 5.02 | 22261 | 26 |
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 | 2.2 | 2.28 | 100 | 0.321 | 0.321 | 3.6 | 4.96 | 2200 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.2 | 41.24 | 21123 | 1136 | 99.97 | 0.17511 | 0.17203 | 0.23341 | RANDOM | 25.671 |
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] | |
-0.15 | -0.08 | -0.15 | 0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.336 |
r_dihedral_angle_4_deg | 18.101 |
r_dihedral_angle_3_deg | 14.528 |
r_dihedral_angle_1_deg | 6.711 |
r_scangle_it | 4.5 |
r_scbond_it | 2.79 |
r_angle_refined_deg | 1.77 |
r_mcangle_it | 1.537 |
r_mcbond_it | 0.852 |
r_metal_ion_refined | 0.495 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2511 |
Nucleic Acid Atoms | |
Solvent Atoms | 271 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
REFMAC | refinement |
CrystalClear | data reduction |
CrystalClear | data scaling |