5LA2
The mechanism by which arabinoxylanases can recognise highly decorated xylans
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5AK1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293.15 | 100 mM Tris-Bicine buffer pH 8.5, 12.5% (w/v) polyethylene glycol average Mw 1,000 Da, 12.5% (w/v) polyethylene glycol average Mw 3,350 Da and 12.5% (RS)-2-methyl-2,4-pentanediol (racemic). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.72 | 54.79 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 76.273 | ¦Á = 90 |
b = 123.176 | ¦Â = 90 |
c = 125.38 | ¦Ã = 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 PILATUS3 6M | 2015-09-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.9791 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.65 | 48.43 | 99.8 | 0.057 | 0.988 | 11.2 | 3.3 | 140288 | 1.5 |
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 | 1.68 | 99.4 | 0.749 | 1.6 | 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 | 5AK1 | 1.65 | 48.43 | 133265 | 6940 | 98.6 | 0.14901 | 0.14637 | 0.19855 | RANDOM | 21.695 |
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] | |
-0.59 | 0.7 | -0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 34.455 |
r_dihedral_angle_2_deg | 33.549 |
r_dihedral_angle_4_deg | 16.097 |
r_dihedral_angle_3_deg | 11.761 |
r_sphericity_bonded | 9.352 |
r_dihedral_angle_1_deg | 6.39 |
r_long_range_B_refined | 4.771 |
r_long_range_B_other | 3.891 |
r_scangle_other | 2.94 |
r_mcangle_other | 2.596 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7241 |
Nucleic Acid Atoms | |
Solvent Atoms | 923 |
Heterogen Atoms | 118 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
MOLREP | phasing |
XDS | data reduction |
XDS | data scaling |