4WMI
Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex I)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.063 | α = 90 |
b = 89.063 | β = 90 |
c = 42.741 | γ = 120 |
Symmetry | |
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Space Group | P 3 |
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 6M | 2014-06-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.1000 | NSLS | X25 |
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 | 1.87 | 77.13 | 99.6 | 0.084 | 19.2 | 8.9 | 31390 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.87 | 1.94 | 96.4 | 0.58 | 2 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.87 | 77.13 | 29692 | 1570 | 99.58 | 0.19634 | 0.19477 | 0.22565 | RANDOM | 30.483 |
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] | |
-0.33 | -0.16 | -0.33 | 0.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.674 |
r_dihedral_angle_4_deg | 16.672 |
r_dihedral_angle_3_deg | 15.839 |
r_dihedral_angle_1_deg | 5.466 |
r_angle_refined_deg | 1.399 |
r_chiral_restr | 0.098 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2703 |
Nucleic Acid Atoms | |
Solvent Atoms | 120 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |