3JUL
Crystal structure of Listeria innocua D-Tagatose-6-Phosphate Kinase bound with substrate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.5 | 298 | 25% PEG 3350, 0.2M MgCl2, 0.1M Tris pH 8.5, 8mM Fructose-6-Phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.307 | α = 90 |
b = 44.24 | β = 104.65 |
c = 79.116 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 210 | MIRRORS | 2009-08-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12C | NSLS | X12C |
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 | 2.2 | 50 | 99.1 | 0.097 | 7.9 | 6.4 | 14658 | 21.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.2 | 2.28 | 94.3 | 0.591 | 5.3 | 5.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB ENTRY 3HIC | 2.4 | 40.78 | 10640 | 10640 | 439 | 94.5 | 0.226 | 0.226 | 0.267 | RANDOM | 35.2 |
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] | |
-6.177 | 11.758 | 5.576 | 0.601 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 3.242 |
c_mcangle_it | 2.325 |
c_scbond_it | 2.324 |
c_mcbond_it | 1.377 |
c_angle_deg | 1.3 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2265 |
Nucleic Acid Atoms | |
Solvent Atoms | 80 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
MOLREP | phasing |
CNS | refinement |
DENZO | data reduction |
HKL-2000 | data scaling |