4MZU
Crystal structure of FdtD, a bifunctional ketoisomerase/N-acetyltransferase from Shewanella denitrificans
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 100 mM HEPPS, 7-12% PEG-8000, 100 mM MgCl2, 10 mM dTDP, 10 mM CoA, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.314 | α = 79.23 |
b = 109.443 | β = 79.98 |
c = 127.847 | γ = 84.89 |
Symmetry | |
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Space Group | P 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 210r | mirrors | 2012-12-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.9794 | APS | 19-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 30 | 91.1 | 0.071 | 0.071 | 27 | 3 | 205722 | 205772 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.2 | 2.28 | 87 | 0.223 | 0.223 | 4.7 | 2.5 | 19668 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | model from SAD experiment | 2.2 | 30 | 205772 | 195488 | 10284 | 90.88 | 0.20751 | 0.20751 | 0.20421 | 0.26985 | RANDOM | 35.626 |
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] | |
0.45 | 1.16 | 0.58 | -2.13 | 0.57 | 1.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.011 |
r_dihedral_angle_4_deg | 23.834 |
r_dihedral_angle_3_deg | 19.948 |
r_dihedral_angle_1_deg | 7.804 |
r_scangle_it | 5.063 |
r_scbond_it | 3.287 |
r_angle_refined_deg | 2.23 |
r_mcangle_it | 2.051 |
r_mcbond_it | 1.133 |
r_chiral_restr | 0.153 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 26574 |
Nucleic Acid Atoms | |
Solvent Atoms | 847 |
Heterogen Atoms | 962 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
SOLVE | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |