5T9F
Prephenate Dehydrogenase N222D mutant from Soybean
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | 2 mM of an oxometalates solution containing 0.005 M sodium chromate tetrahydrate, 0.005 M sodium molybdate dihydrate, 0.005M sodium tungstate dihydrate, and 0.005 M sodium orthovanadate, 0.1 M of MOPSO and Bis-Tris, pH 6.5, and 50% v/v of a precipitant mixture of 20% w/v PEG 8000 and 40% v/v 1,5-pentanediol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 52.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.445 | α = 107.82 |
b = 55.046 | β = 99.56 |
c = 68.387 | γ = 102.58 |
Symmetry | |
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Space Group | P 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 | PIXEL | DECTRIS PILATUS3 S 6M | 2016-07-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.98 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.994 | 33.85 | 88.9 | 10.19 | 1.7 | 36694 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.994 | 2.048 | 85.3 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | FREE R-VALUE | 1.994 | 33.846 | 1.98 | 36686 | 1832 | 88.38 | 0.1602 | 0.1579 | 0.2058 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.333 |
f_angle_d | 0.912 |
f_chiral_restr | 0.054 |
f_bond_d | 0.008 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3988 |
Nucleic Acid Atoms | |
Solvent Atoms | 435 |
Heterogen Atoms | 122 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-3000 | data collection |
SCALEPACK | data scaling |
PHASER | phasing |