5M7D
Blood group synthase AAGlyB in complex with UDP-Gal and cryoprotected with glycerol
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | MOPS buffer, manganese chloride, ammonium sulfate, PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.44 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 52.643 | ¦Á = 90 |
b = 148.796 | ¦Â = 90 |
c = 79.782 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 2 2 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2015-08-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.0723 | ESRF | ID29 |
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 | 1.2 | 42.14 | 99.1 | 0.088 | 10.4 | 3.5 | 96982 |
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 | 1.2 | 1.22 | 99.3 | 0.522 | 2.1 | 3.3 |
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 | FOURIER SYNTHESIS | FREE R-VALUE | 1.2 | 40 | 92055 | 4900 | 98.98 | 0.13163 | 0.13033 | 0.15654 | RANDOM | 12.791 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.5 | 0.49 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.336 |
r_dihedral_angle_4_deg | 18.859 |
r_dihedral_angle_3_deg | 12.461 |
r_sphericity_bonded | 7.298 |
r_dihedral_angle_1_deg | 6.648 |
r_rigid_bond_restr | 4.942 |
r_sphericity_free | 4.072 |
r_long_range_B_refined | 2.554 |
r_long_range_B_other | 2.042 |
r_scangle_other | 2.025 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2427 |
Nucleic Acid Atoms | |
Solvent Atoms | 362 |
Heterogen Atoms | 71 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
REFMAC | phasing |