6O9F
The structure of Thermomyces Lanuginosa lipase in complex with 1,3 diacylglycerol in a monoclinic crystal form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | Protein source was a filtered fungal culture medium at about 50 mg/ml. This was combined in 8 ul drops with equal amounts of 25% PEG 3350 buffered at pH 6.5 with 0.10 M MES and crystallized at room temperature by sitting drops in Cryschem plates |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.185 | α = 90 |
b = 91.366 | β = 94.705 |
c = 124.316 | 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 | 293 | CCD | RIGAKU SATURN 944 | 2016-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5419 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.48 | 80 | 100 | 0.292 | 0.245 | 0.327 | 0.102 | 0.979 | 7.1 | 9.6 | 81074 | 27.29 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2.48 | 2.52 | 96.2 | 1.02 | 0.85 | 1.3 | 0.623 | 0.18 | 1.3 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | 2.48 | 51.27 | 1.34 | 61661 | 3025 | 99.54 | 0.1768 | 0.1749 | 0.2145 | RANDOM | 32.59 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.4491 |
f_angle_d | 0.5208 |
f_chiral_restr | 0.0418 |
f_plane_restr | 0.0039 |
f_bond_d | 0.0025 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12425 |
Nucleic Acid Atoms | |
Solvent Atoms | 428 |
Heterogen Atoms | 431 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
PHASER | phasing |