4YTR
Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 1-deoxy L-tagatose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293 | 6-9 % PEG4000, 0.1 M Sodium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.38 | α = 90 |
b = 126.33 | β = 98.7 |
c = 92.92 | 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 | 100 | IMAGE PLATE | RIGAKU RAXIS VII | 2012-10-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
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 | 1.9 | 22.14 | 98.2 | 0.085 | 8.7 | 2.92 | 92108 | 15.9 |
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 | 1.9 | 1.97 | 85.2 | 0.299 | 3.4 | 2.45 | 7957 |
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 | 2QUL | 1.9 | 21.71 | 92074 | 9204 | 98 | 0.193 | 0.188 | 0.235 | RANDOM | 21 |
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] | |
-1.94 | -1.37 | -0.65 | 2.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.4 |
c_scangle_it | 2.73 |
c_scbond_it | 1.96 |
c_mcangle_it | 1.79 |
c_mcbond_it | 1.21 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.77 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9283 |
Nucleic Acid Atoms | |
Solvent Atoms | 1151 |
Heterogen Atoms | 114 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
d*TREK | data reduction |
PDB_EXTRACT | data extraction |
CrystalClear | data scaling |
MOLREP | phasing |