2XIG
The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.4 | HPFUR2M PRE-LOADED WITH ZINC (2 EQ) AT 30 MG/ML WAS CRYSTALLIZED FROM 20% PEG 3350, 100 MM NA CITRATE, pH 7.4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 45.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.15 | α = 83.32 |
b = 48.29 | β = 77.82 |
c = 72.25 | γ = 87.65 |
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 | CCD | ADSC QUANTUM 315 | TOROIDAL MIRROR | 2009-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 1.85 | 47.96 | 95.2 | 0.1 | 4.5 | 4.1 | 51362 | 6 | 23.58 |
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 | 1.85 | 1.95 | 94.8 | 0.39 | 1.8 | 4.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | ZN-SAD MODEL AT 2.15A | 1.85 | 35.097 | 1.96 | 99642 | 5032 | 92.4 | 0.1999 | 0.1981 | 0.2339 | 35.66 |
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] | |
5.3609 | 3.9897 | -2.2187 | 4.5069 | -2.4059 | -9.8678 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.233 |
f_angle_d | 0.87 |
f_chiral_restr | 0.061 |
f_bond_d | 0.005 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4780 |
Nucleic Acid Atoms | |
Solvent Atoms | 377 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |