6WFV
The crystal structure of a collagen galactosylhydroxylysyl glucosyltransferase from human
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose |
2 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose, crystal soaked in higher Mn and UDP-Glc prior to flash cooling. |
3 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose. Crystal soaked in 1 M NaI prior to flash cooling |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.066 | α = 90 |
b = 71.066 | β = 90 |
c = 110.813 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | PIXEL | DECTRIS PILATUS3 6M | 2016-06-02 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2016-10-12 | M | SINGLE WAVELENGTH | ||||||
3 | 3 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2016-09-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.1271 | ALS | 8.3.1 |
2 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.1158 | ALS | 8.3.1 |
3 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.7136 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.7 | 41.18 | 99.7 | 0.117 | 0.12 | 0.999 | 19.67 | 17.521 | 36393 | 31.679 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.7 | 1.74 | 96.4 | 1.64 | 1.73 | 0.717 | 2.1 | 9.969 |
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 | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | SIRAS | THROUGHOUT | 1.7 | 41.18 | 35211 | 1931 | 96.48 | 0.1528 | 0.1516 | 0.1722 | 34.1078 |
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 | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.7149 |
f_angle_d | 1.172 |
f_chiral_restr | 0.0532 |
f_bond_d | 0.0097 |
f_plane_restr | 0.0065 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1892 |
Nucleic Acid Atoms | |
Solvent Atoms | 229 |
Heterogen Atoms | 79 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
SHELXD | phasing |
SOLVE | phasing |
RESOLVE | model building |
SHELXE | model building |
Coot | model building |
PDB_EXTRACT | data extraction |