5A94
Crystal structure of beta-Glucanase SdGluc5_26A from Saccharophagus degradans in complex with tetrasaccharide A, form 1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 30% (W/V) PEG 4000, 0.1 M TRIS BUFFER PH 7.5, 0.2 M MGCL2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 188.643 | α = 90 |
b = 132.753 | β = 133.78 |
c = 131.352 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 PILATUS 6M | 2013-09-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | SOLEIL | PROXIMA 1 |
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 | 2 | 47.53 | 100 | 0.1 | 6.6 | 3.5 | 157114 | 19.67 |
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 | 2 | 2.11 | 99.9 | 0.37 | 2.6 | 3.6 |
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 | WWPDB ENTRY 5A8N | 1.99 | 47.42 | 149108 | 8001 | 98.22 | 0.1795 | 0.17891 | 0.19038 | RANDOM | 23.785 |
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] | |
-0.93 | 14.92 | -5.41 | 6.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.022 |
r_dihedral_angle_4_deg | 15.511 |
r_dihedral_angle_3_deg | 12.529 |
r_dihedral_angle_1_deg | 5.655 |
r_angle_refined_deg | 1.282 |
r_angle_other_deg | 1.15 |
r_symmetry_vdw_refined | 0.31 |
r_symmetry_vdw_other | 0.257 |
r_nbd_refined | 0.241 |
r_symmetry_hbond_refined | 0.235 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16604 |
Nucleic Acid Atoms | |
Solvent Atoms | 1541 |
Heterogen Atoms | 216 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |