7B4J
Thermostable omega transaminase PjTA-R6 variant W58M/F86L/R417L engineered for asymmetric synthesis of enantiopure bulky amines
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.6 | 293 | Drop were prepared by mixing 1ul of protein solution (~10 mg/ml in 20 mM HEPES pH 7.5, 100 mM NaCl, and 20 uM PLP buffer ) with 1ul of reservoir solution. The reservoir contained 0.7-1M Succinic acid pH 7.6. Crystals formed after 48h. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 56.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.822 | α = 90 |
b = 97.822 | β = 90 |
c = 118.716 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
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 | PIXEL | DECTRIS EIGER2 XE 16M | 2019-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.9 | 50.8 | 100 | 0.054 | 0.06 | 0.027 | 0.999 | 15.1 | 4.9 | 87797 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.9 | 1.93 | 100 | 0.737 | 0.826 | 0.368 | 0.7 | 4.9 |
Refinement
Statistics | |||||||||||||||||||
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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 | FOURIER SYNTHESIS | FREE R-VALUE | 1.9 | 50.8 | 83494 | 4254 | 99.99 | 0.1792 | 0.1778 | 0.2076 | RANDOM | 33.469 |
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] | |
0.07 | 0.07 | -0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.799 |
r_dihedral_angle_4_deg | 14.957 |
r_dihedral_angle_3_deg | 12.902 |
r_dihedral_angle_1_deg | 6.899 |
r_angle_refined_deg | 1.458 |
r_angle_other_deg | 1.399 |
r_chiral_restr | 0.075 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6901 |
Nucleic Acid Atoms | |
Solvent Atoms | 398 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DIALS | data processing |
Coot | model building |
REFMAC | phasing |
xia2 | data processing |