3PFB
Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with ethylferulate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 298 | 0.1 M Tris pH 8.5, 0.2 M ammonium sulphate, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.26 | α = 90 |
b = 83.891 | β = 98.21 |
c = 88.947 | 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 | IMAGE PLATE | RIGAKU RAXIS HTC | mirrors | 2009-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.5418 |
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 | 1.58 | 50 | 73.1 | 0.046 | 31.21 | 2 | 52487 | 52487 | -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) | |||||||||||
1 | 1.58 | 1.61 | 21.6 | 0.26 | 3.09 | 1.3 | 769 |
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 | Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant | 1.58 | 44.2 | 49803 | 2673 | 73.06 | 0.21609 | 0.2113 | 0.30439 | RANDOM | 26.599 |
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] | |
0.65 | 0.04 | -1.61 | 0.97 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.66 |
r_dihedral_angle_4_deg | 20.668 |
r_dihedral_angle_3_deg | 15.05 |
r_dihedral_angle_1_deg | 6.86 |
r_scangle_it | 5.708 |
r_scbond_it | 4.285 |
r_mcangle_it | 2.393 |
r_rigid_bond_restr | 2.268 |
r_angle_refined_deg | 1.933 |
r_mcbond_it | 1.698 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3908 |
Nucleic Acid Atoms | |
Solvent Atoms | 907 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |