7CW1
Crystal structure of a biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast, Pseudozyma antarctica, solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 0.17M Sodium acetate trihydrate, 0.085M Sodium cacodylate trihydrate , 25.5%w/v Polyethylene glycol 8000, 15%w/v Polyethylene glycol 400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.839 | 33.157 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.065 | α = 90 |
b = 61.587 | β = 90 |
c = 110.387 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2017-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.7 | 55.19 | 98.3 | 0.117 | 0.122 | 0.034 | 0.998 | 17 | 12.9 | 33315 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.7 | 1.73 | 96 | 0.487 | 0.507 | 0.139 | 0.933 | 12.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.7 | 55.19 | 31548 | 1713 | 98.09 | 0.1576 | 0.1558 | 0.1911 | RANDOM | 9.31 |
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] | |
-0.14 | -0.27 | 0.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.162 |
r_dihedral_angle_4_deg | 19.603 |
r_dihedral_angle_3_deg | 11.061 |
r_dihedral_angle_1_deg | 6.673 |
r_angle_refined_deg | 1.684 |
r_angle_other_deg | 1.594 |
r_chiral_restr | 0.096 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2846 |
Nucleic Acid Atoms | |
Solvent Atoms | 361 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
xia2 | data reduction |
CRANK2 | phasing |