5ADW
The Periplasmic Binding Protein CeuE of Campylobacter jejuni preferentially binds the iron(III) complex of the Linear Dimer Component of Enterobactin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ZKW | PDB ENTRY 3ZKW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 0.1 M MMT (DL-MALIC ACID, MES, TRIS, 1:2:2) BUFFER, PH 8.0, 25% (W/V) PEG 1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.461 | α = 83.36 |
b = 63.021 | β = 76.57 |
c = 67.011 | γ = 78.24 |
Symmetry | |
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Space Group | P 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 PILATUS 2M | 2014-03-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.9 | 45.76 | 98.1 | 0.1 | 17.5 | 4.4 | 70279 | 2 |
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 | 1.9 | 1.94 | 96.1 | 0.9 | 2.2 | 4.2 |
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 | PDB ENTRY 3ZKW | 1.9 | 65.01 | 66562 | 3495 | 97.78 | 0.22676 | 0.2248 | 0.26407 | RANDOM | 42.232 |
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] | |
-1.58 | -1.62 | 0.39 | -1.11 | 0.99 | 2.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.449 |
r_dihedral_angle_4_deg | 18.855 |
r_dihedral_angle_3_deg | 16.108 |
r_long_range_B_refined | 8.083 |
r_long_range_B_other | 8.082 |
r_dihedral_angle_1_deg | 6.583 |
r_scangle_other | 6.304 |
r_mcangle_it | 5.315 |
r_mcangle_other | 5.314 |
r_scbond_it | 4.415 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6581 |
Nucleic Acid Atoms | |
Solvent Atoms | 130 |
Heterogen Atoms | 81 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |