6VHV
Klebsiella oxytoca NpsA in complex with 3-hydroxyanthranilyl-AMSN
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6.6 | 296 | well solution: 400 mM imidazole pH 6.6, 10% w/v PEG8000/10000/12000/20000, 2.5% w/v 1,3-dimethylimidazolium dimethyl phosphate protein solution (16 mg/mL): 10 mM HEPES pH 8.0, 25 mM NaCl, 0.4 mM TCEP, 5 mM 3HA-AMSN droplet: 2 uL protein solution, 1 uL well solution |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.689 | α = 90 |
b = 87.817 | β = 90 |
c = 165.778 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 PILATUS3 6M | 2019-03-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.03322 | APS | 23-ID-D |
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) | CC (Half) | 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 | 2.89 | 68.1 | 99.9 | 0.149 | 0.163 | 0.063 | 0.997 | 9.4 | 6.5 | 12516 | 86.74 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.89 | 2.95 | 100 | 2.088 | 2.261 | 0.858 | 0.412 | 0.9 | 6.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 | FREE R-VALUE | 6vhu | 2.89 | 68.1 | 1.34 | 12507 | 604 | 99.81 | 0.2198 | 0.2176 | 0.262 | 97.58 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.5826 |
f_angle_d | 0.5558 |
f_chiral_restr | 0.0467 |
f_plane_restr | 0.0046 |
f_bond_d | 0.0038 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3672 |
Nucleic Acid Atoms | |
Solvent Atoms | 8 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
autoPROC | data scaling |
PHASER | phasing |
Coot | model building |
PHENIX | refinement |