6XQH
Crystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with cellotriose, presenting a 1,3-beta-D-cellobiosyl-glucose and a cellobiose at active site
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6XOF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 291 | 27.5 % PEG4000, 0.2 M magnesium chloride, and 0.1 M MES, pH 5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.85 | 33.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.729 | α = 90 |
b = 49.745 | β = 90 |
c = 115.261 | 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 | 100 | PIXEL | DECTRIS PILATUS 2M | 2015-11-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | 1.4586 | LNLS | W01B-MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.57 | 49.74 | 99.1 | 0.075 | 0.079 | 0.024 | 0.999 | 22.1 | 10 | 31767 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.57 | 1.6 | 82.3 | 0.302 | 0.334 | 0.139 | 0.933 | 5.3 |
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 | 6XOF | 1.57 | 45.71 | 30152 | 1526 | 99.15 | 0.1522 | 0.1503 | 0.1915 | RANDOM | 9.152 |
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] | |
-0.42 | 0.25 | 0.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.623 |
r_dihedral_angle_4_deg | 15.714 |
r_dihedral_angle_3_deg | 12.258 |
r_dihedral_angle_1_deg | 7.7 |
r_angle_refined_deg | 2.012 |
r_angle_other_deg | 1.628 |
r_chiral_restr | 0.095 |
r_bond_refined_d | 0.017 |
r_gen_planes_refined | 0.013 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2050 |
Nucleic Acid Atoms | |
Solvent Atoms | 473 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
XDS | data reduction |