6GWG
Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose covalently linked to the nucleophile
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5M0X |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.2 M magnesium sulfate, 20% (w/v) PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.73 | α = 90 |
b = 95.87 | β = 90 |
c = 97.44 | 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 PILATUS 6M | 2017-01-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.976 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.77 | 24.36 | 99.9 | 0.118 | 0.074 | 0.997 | 9 | 6.6 | 61617 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.77 | 1.82 | 56.4 | 1.438 | 0.903 | 0.564 | 1.1 | 6.7 |
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 | 5M0X | 1.77 | 24.36 | 58648 | 2901 | 99.91 | 0.16969 | 0.16738 | 0.21495 | RANDOM | 27.819 |
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] | |
2.38 | -1.69 | -0.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.647 |
r_dihedral_angle_4_deg | 20.99 |
r_dihedral_angle_3_deg | 14.942 |
r_dihedral_angle_1_deg | 7.467 |
r_long_range_B_refined | 6.811 |
r_long_range_B_other | 6.81 |
r_scangle_other | 5.475 |
r_scbond_it | 3.834 |
r_scbond_other | 3.834 |
r_mcangle_it | 3.384 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4276 |
Nucleic Acid Atoms | |
Solvent Atoms | 470 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |