5DIY
Thermobaculum terrenum O-GlcNAc hydrolase mutant - D120N
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 295 | 38% PEG-4000, 400 mM sodium acetate, 0.1 M Tris-HCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 42.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 161.176 | α = 90 |
b = 52.55 | β = 122.35 |
c = 131.511 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 80 | PIXEL | PSI PILATUS 6M | 2014-01-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.976 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.06 | 49.03 | 99.6 | 0.072 | 12.5 | 4.1 | 237569 | 57769 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.06 | 2.13 | 98.9 | 0.69 | 1.8 | 4.1 |
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 | THROUGHOUT | 2.06 | 49.03 | 54843 | 2923 | 99.54 | 0.20238 | 0.20054 | 0.23633 | RANDOM | 32.583 |
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] | |
1.27 | -0.17 | 0.3 | -0.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.059 |
r_dihedral_angle_4_deg | 20.312 |
r_dihedral_angle_3_deg | 13.334 |
r_dihedral_angle_1_deg | 5.785 |
r_long_range_B_refined | 3.58 |
r_long_range_B_other | 3.53 |
r_scangle_other | 2.136 |
r_mcangle_it | 1.906 |
r_mcangle_other | 1.906 |
r_scbond_it | 1.245 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7709 |
Nucleic Acid Atoms | |
Solvent Atoms | 297 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |