4P47
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM OCHROBACTRUM ANTHROPI (Oant_4429), TARGET EFI-510151, C-TERMIUS BOUND IN LIGAND BINDING POCKET
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | Protein (40.24 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (0.2 M Ammonium Sulfate, 20 %(w/v) PEG 3350); Cryoprotection (20% ethylene glycol, 80% reservoir) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.87 | 34.19 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 54.183 | ¦Á = 90 |
b = 68.695 | ¦Â = 90 |
c = 76.431 | ¦Ã = 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 | CCD | RAYONIX MX225HE | MIRRORS | 2013-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9793 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.3 | 25.535 | 99.6 | 0.108 | 0.116 | 0.043 | 9.9 | 7 | 70496 | 70496 | 10.59 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.3 | 1.37 | 98.6 | 0.782 | 0.782 | 0.331 | 1 | 6.2 | 10037 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | FREE R-VALUE | 1.3 | 23.935 | 1.34 | 70429 | 3562 | 99.49 | 0.1648 | 0.1635 | 0.188 | Random Selection | 14.88 |
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 | 13.367 |
f_angle_d | 1.253 |
f_chiral_restr | 0.07 |
f_bond_d | 0.009 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2492 |
Nucleic Acid Atoms | |
Solvent Atoms | 491 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
PHENIX | refinement |