5FKT
Unraveling the first step of xyloglucan degradation by the soil saprophyte Cellvibrio japonicus through the functional and structural characterization of a potent GH74 endo-xyloglucanase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.1 M SODIUM ACETATE (PH 5.0), 0.6 M SODIUM FORMATE, 8 % W/V PGA-LM |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.12 | α = 90 |
b = 94.29 | β = 103.2 |
c = 105.56 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 120 | PIXEL | DECTRIS PILATUS | 2015-02-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
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 | 1.52 | 69.48 | 99.9 | 0.09 | 10.7 | 4.1 | 245787 | 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 | 1.52 | 1.56 | 99.9 | 0.72 | 1.7 | 4.1 |
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 5FKR | 1.52 | 69.48 | 233635 | 12120 | 99.9 | 0.16858 | 0.16726 | 0.19384 | RANDOM | 12.946 |
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] | |
0.12 | 0.38 | -0.09 | -0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.048 |
r_dihedral_angle_4_deg | 16.787 |
r_dihedral_angle_3_deg | 11.164 |
r_dihedral_angle_1_deg | 7.23 |
r_angle_refined_deg | 1.891 |
r_scbond_it | 1.769 |
r_mcangle_it | 1.672 |
r_mcbond_it | 1.168 |
r_mcbond_other | 1.159 |
r_angle_other_deg | 1.083 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11083 |
Nucleic Acid Atoms | |
Solvent Atoms | 1277 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
MOLREP | phasing |