5M7S
Structure of human O-GlcNAc hydrolase with bound transition state analog ThiametG
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 292 | 0.1-0.2 M tri ammonium citrate pH 7.5 16-20 % PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.45 | 49.9 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 101.908 | ¦Á = 90 |
b = 101.908 | ¦Â = 90 |
c = 282.799 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 6M | 2016-04-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.979 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 2.4 | 96.06 | 100 | 0.121 | 0.035 | 13.4 | 12.6 | 59331 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.4 | 2.47 | 100 | 2.857 | 0.847 | 0.463 | 1 | 11.7 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.4 | 96.06 | 59286 | 1770 | 99.95 | 0.2078 | 0.207 | 0.2322 | RANDOM | 78.1132 |
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] | |
-0.22 | -0.22 | 0.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.415 |
r_dihedral_angle_4_deg | 18.978 |
r_dihedral_angle_3_deg | 18.21 |
r_dihedral_angle_1_deg | 6.411 |
r_angle_other_deg | 3.652 |
r_mcangle_it | 2.169 |
r_angle_refined_deg | 1.609 |
r_mcbond_it | 1.267 |
r_mcbond_other | 1.267 |
r_chiral_restr | 0.104 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7260 |
Nucleic Acid Atoms | |
Solvent Atoms | 25 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
REFMAC | phasing |