7YLZ
Unliganded form of hydroxyamidotransferase TsnB9
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 30% (w/v) PEG 8,000, 0.2 M ammonium sulfate, and 0.1 M sodium cacodylate trihydrate (pH 6.5) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.68 | α = 101.153 |
b = 76.57 | β = 114.435 |
c = 82.14 | γ = 109.556 |
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-F | 2020-12-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1.000 | Photon Factory | AR-NE3A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (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 | 2.72 | 50 | 91.8 | 0.099 | 0.986 | 6.42 | 1.9 | 64632 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.72 | 2.79 | 0.615 | 0.702 | 1.14 |
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 | AlphaFold model | 2.72 | 33.611 | 33710 | 1691 | 96.207 | 0.268 | 0.2661 | 0.2937 | 35.863 |
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] | |
0.407 | 0.538 | -1.021 | 3.152 | 0.37 | -1.944 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 26.749 |
r_dihedral_angle_3_deg | 13.758 |
r_dihedral_angle_4_deg | 13.594 |
r_dihedral_angle_1_deg | 5.091 |
r_lrange_it | 1.363 |
r_lrange_other | 1.363 |
r_angle_refined_deg | 1.187 |
r_angle_other_deg | 1.086 |
r_mcangle_it | 0.389 |
r_mcangle_other | 0.389 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8691 |
Nucleic Acid Atoms | |
Solvent Atoms | 46 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |