8P20
TarM(Se)_G117R-UDP-4RboP-glucose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.9 | 293 | 10% PEG 20 000, 25% PEG MME 550, 0.1 M MES/imidazole, pH 6.9, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium tartrate (racemic), 0.02 M sodium oxamate. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.62 | α = 90.015 |
b = 75.75 | β = 90.039 |
c = 129.4 | γ = 90.031 |
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 PILATUS 2M | 2020-12-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.9998671568878699 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.848 | 49.23 | 99.9 | 0.99 | 5.8 | 4.6 | 51972 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.848 | 2.92 | 100 | 0.41 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MIR | FREE R-VALUE | 2.848 | 49.204 | 51971 | 2691 | 99.752 | 0.23 | 0.2283 | 0.2664 | 48.793 |
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] | |
-13.915 | 15.052 | -5.92 | 55.116 | 31.486 | -41.201 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.622 |
r_dihedral_angle_3_deg | 22.562 |
r_dihedral_angle_4_deg | 22.021 |
r_lrange_it | 5.399 |
r_lrange_other | 5.399 |
r_dihedral_angle_1_deg | 3.803 |
r_mcangle_it | 3.074 |
r_mcangle_other | 3.074 |
r_scangle_it | 2.504 |
r_scangle_other | 2.504 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14004 |
Nucleic Acid Atoms | |
Solvent Atoms | 734 |
Heterogen Atoms | 423 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |