5HSG
Crystal structure of an ABC transporter Solute Binding Protein from Klebsiella pneumoniae (KPN_01730, target EFI-511059), APO open structure
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM L-sorbitol); Reservoir (MCSG1 B4)(0.2 M Magnesium Chloride, 0.1 M Bis-Tris pH 6.5, 25 %(w/v) PEG 3350); Cryoprotection (20% Diethylene Glycol, 80% Reservoir) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.548 | α = 90 |
b = 48.8 | β = 90 |
c = 157.115 | γ = 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 | 2015-10-20 | 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 Merge 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 | 100 | 93 | 0.092 | 0.095 | 0.026 | 8.2 | 12.8 | 70639 | 13.83 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.3 | 1.32 | 87.2 | 0.876 | 0.91 | 0.242 | 0.86 | 13.2 | 3302 |
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 | FREE R-VALUE | 1.3 | 30.725 | 1.34 | 68101 | 3363 | 89.79 | 0.1512 | 0.15 | 0.174 | 19.1155 |
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 | 13.09 |
f_angle_d | 1.242 |
f_chiral_restr | 0.071 |
f_bond_d | 0.009 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2096 |
Nucleic Acid Atoms | |
Solvent Atoms | 497 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
SHELX | phasing |
MLPHARE | phasing |
HKL-3000 | data reduction |