4GYY
Crystal structure of human O-GlcNAc Transferase with UDP-5SGlcNAc and a peptide substrate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 1.6M Lithium Sulfate, 0.1M Bis Tris Propane pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.03 | 59.42 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 98.52 | ¦Á = 90 |
b = 136.48 | ¦Â = 103.51 |
c = 152.77 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | PSI PILATUS 6M | 2011-12-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.000 | NSLS | X25 |
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 | 1.85 | 59.95 | 99.7 | 166242 | 166242 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.85 | 1.95 | 99.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.85 | 59.946 | 1.35 | 166242 | 166049 | 8349 | 99.51 | 0.2187 | 0.2187 | 0.2177 | 0.2374 | RANDOM |
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] | |
1.9363 | 8.2616 | -6.7918 | 4.8556 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.535 |
f_angle_d | 0.806 |
f_chiral_restr | 0.056 |
f_bond_d | 0.004 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10972 |
Nucleic Acid Atoms | |
Solvent Atoms | 836 |
Heterogen Atoms | 93 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
PHENIX | model building |
PHENIX | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHENIX | phasing |