6PXU
Crystal structure of human GalNAc-T12 bound to a diglycosylated peptide, Mn2+, and UDP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.2 M sodium chloride, 20% w/v PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.82 | α = 113.08 |
b = 73.123 | β = 100.5 |
c = 74.441 | γ = 108.23 |
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 | CCD | MARMOSAIC 225 mm CCD | 2017-06-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1 | APS | 22-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | 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 | 2.007 | 20.03 | 97 | 0.197 | 0.1 | 4.7 | 1 | 163130 | 29.33 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.007 | 2.03 | 89.5 | 0.903 | 0.339 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2FFU | 2.007 | 20.027 | 1.73 | 163130 | 7888 | 97.1 | 0.1734 | 0.1711 | 0.2189 | 42.0352 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.443 |
f_angle_d | 0.981 |
f_chiral_restr | 0.059 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8846 |
Nucleic Acid Atoms | |
Solvent Atoms | 562 |
Heterogen Atoms | 206 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
MOLREP | phasing |