6TRF
Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) purified from cells treated with kifunensine.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5NV4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 0.03M Sodium nitrate, 0.03 Sodium phosphate dibasic, 0.03M Ammonium sulfate; Tris Bicine pH 8.5; 40% v/v Glycerol, 20% w/v PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.29 | 62.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.655 | α = 90 |
b = 148.928 | β = 90 |
c = 190.298 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | DECTRIS PILATUS3 2M | 2016-05-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 4.106 | 95.149 | 90.2 | 0.149 | 0.157 | 0.047 | 0.997 | 9.9 | 10.9 | 7500 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 4.106 | 4.493 | 72.4 | 3.268 | 3.376 | 0.836 | 0.566 | 1.3 | 15.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 5nv4 | 4.106 | 95.149 | 7500 | 351 | 40.7 | 0.2577 | 0.2551 | 0.3154 | RANDOM | 270.25 |
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] | |
26.1611 | -63.1082 | 36.947 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 19.8 |
t_omega_torsion | 2.7 |
t_angle_deg | 0.95 |
t_bond_d | 0.006 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10616 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 101 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
STARANISO | data scaling |
PHASER | phasing |