4P07
Bacterial aryl sulfotransferase (ASST) soaked with human urine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ELQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | Sitting drop vapor diffusion method by equilibrating 1.5 ?l of protein solution (22 mg/ml, in 20 mM 4-morpholinepropanesulfonic acid/NaOH pH 7.5, 100 mM NaCl) with 0.5 ?l of reservoir solution consisting of 1.8 M Li2SO4 and 100 mM cacodylic acid/NaOH pH 6.5. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.82 | 67.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 182.295 | α = 90 |
b = 182.295 | β = 90 |
c = 101.592 | γ = 120 |
Symmetry | |
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Space Group | P 32 1 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 | PIXEL | DECTRIS PILATUS 6M | 2008-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.000 | SLS | X06SA |
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 | 2.59 | 48.4 | 98.2 | 0.103 | 0.13 | 9.8 | 4.8 | 58584 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.59 | 2.66 | 91.4 | 1.035 | 1.7 | 4.1 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3ELQ | 2.59 | 48.4 | 55613 | 2945 | 98.2 | 0.183 | 0.18 | 0.224 | RANDOM | 47.67 |
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] | |
-2.36 | -2.36 | -2.36 | 7.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.586 |
r_dihedral_angle_3_deg | 15.688 |
r_dihedral_angle_4_deg | 14.451 |
r_dihedral_angle_1_deg | 7.261 |
r_angle_refined_deg | 1.806 |
r_angle_other_deg | 1.18 |
r_chiral_restr | 0.093 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8975 |
Nucleic Acid Atoms | |
Solvent Atoms | 212 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SCALA | data scaling |
XDS | data scaling |
PHASER | phasing |