3L0Q
The crystal structure of xlylulose kinase from Yersinia pseudotuberculosis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GG4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 0.2 M Magnesium chloride, 0.1 M HEPES pH 7.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.876 | α = 90 |
b = 110.005 | β = 99.71 |
c = 80.532 | 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 | 110 | CCD | ADSC QUANTUM 315 | mirrors | 2009-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 0.9792 | NSLS | X25 |
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 | 1.6 | 50 | 92.3 | 0.073 | 9.6 | 1.9 | 126606 | 19.73 |
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) | |||||||||||
1.6 | 1.67 | 90 | 0.686 | 1.1 | 1.9 | 24319 |
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 | 3GG4 | 1.61 | 40.846 | 126606 | 6403 | 92.31 | 0.193 | 0.1915 | 0.2222 | RANDOM | 19.73 |
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] | |
6.6561 | 0.2308 | -3.3304 | -3.3256 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.31 |
f_angle_d | 1.655 |
f_chiral_restr | 0.112 |
f_bond_d | 0.016 |
f_plane_restr | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8326 |
Nucleic Acid Atoms | |
Solvent Atoms | 900 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |