7MFQ
crystal structure of the L136 aminotransferase from acanthamoeba polyphaga mimivirus in complex with the TDP-viosamine external aldimine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | protein incubated with 1 mM PLP and 5 MM TDP-viosamine 18-22% PEG-3350, 2% MPD, 100 mM MES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.21 | α = 90 |
b = 108.515 | β = 90 |
c = 146.058 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | Bruker PHOTON II | 2019-10-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | BRUKER D8 QUEST | 1.54178 |
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 | 1.95 | 50 | 99.8 | 0.09 | 16.2 | 10.7 | 105900 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.95 | 2.05 | 99.7 | 0.411 | 3.5 | 5.1 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7mfp | 1.95 | 29.052 | 105900 | 5323 | 99.829 | 0.176 | 0.1733 | 0.2222 | 14.791 |
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] | |
-0.008 | -0.001 | 0.009 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.333 |
r_dihedral_angle_4_deg | 19.747 |
r_dihedral_angle_3_deg | 14.594 |
r_dihedral_angle_1_deg | 7.009 |
r_lrange_it | 4.33 |
r_lrange_other | 4.33 |
r_scangle_it | 2.588 |
r_scangle_other | 2.588 |
r_mcangle_it | 1.82 |
r_mcangle_other | 1.82 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11178 |
Nucleic Acid Atoms | |
Solvent Atoms | 1236 |
Heterogen Atoms | 226 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SAINT | data reduction |
SADABS | data scaling |
PHASER | phasing |