5BWJ
Structural characterization and modeling of the Borrelia burgdorferi hybrid histidine kinase Hk1 periplasmic sensor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 296 | D1 samples were concentrated to 1.7 mg/ml in 50 mM Tris (pH 7.5), 50 mM NaCl and 1 mM Tris (2-carboxyethyl) phosphine (TCEP). Crystals grown in 0.1M Tris-HCl (pH 8.0), 0.1 M Mg(NO3)2 and 18% PEG 20,000 equilibrated by hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 34.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.3 | α = 90 |
b = 62.853 | β = 101.32 |
c = 111.808 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 6M | 2013-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 0.97910 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.05 | 37.66 | 99.55 | 0.063 | 8.82 | 3.3 | 49534 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.0538 | 2.1052 | 99.03 | 0.554 | 1.79 | 3.1 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.054 | 37.66 | 1.34 | 49524 | 1996 | 99.53 | 0.1945 | 0.1934 | 0.2206 | 54.7777 |
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 | 10.136 |
f_angle_d | 0.641 |
f_chiral_restr | 0.028 |
f_bond_d | 0.003 |
f_plane_restr | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6338 |
Nucleic Acid Atoms | |
Solvent Atoms | 257 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
HKL-2000 | data reduction |
PHASER | phasing |