4D6H
Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 1 blood group A-tetrasaccharide (E558A X02 mutant)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 15% PEG 3350, 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.26 | α = 90 |
b = 154.75 | β = 90 |
c = 97.16 | γ = 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 | IMAGE PLATE | RIGAKU R-AXIS 4 | OSMIC BLUE | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-002 |
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 | 1.65 | 30.7 | 99.9 | 0.07 | 14.2 | 3.8 | 83578 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.65 | 1.74 | 99.3 | 0.5 | 2.2 | 3.4 |
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 | PDB ENTRY 2WMI | 1.65 | 30.16 | 79310 | 4167 | 99.88 | 0.14743 | 0.14541 | 0.18564 | RANDOM | 11.256 |
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] | |
-0.01 | 0.02 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.964 |
r_dihedral_angle_4_deg | 17.715 |
r_dihedral_angle_3_deg | 12.016 |
r_dihedral_angle_1_deg | 6.006 |
r_scangle_it | 3.875 |
r_scbond_it | 2.59 |
r_mcangle_it | 1.52 |
r_angle_refined_deg | 1.294 |
r_rigid_bond_restr | 1.026 |
r_mcbond_it | 0.916 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4775 |
Nucleic Acid Atoms | |
Solvent Atoms | 819 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
Aimless | data scaling |