5OPJ
Beta-L-arabinofuranosidase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 200 mM ammonium formate, 20% PEG 3350, 500 mM L-arabinose |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.21 | α = 90 |
b = 96.21 | β = 90 |
c = 187.84 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | 2017-07-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9796 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.05 | 28.54 | 100 | 0.999 | 17.33 | 72.37 | 56151 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.05 | 2.09 | 100 | 0.831 | 2.11 | 74.92 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.05 | 28.54 | 53209 | 2857 | 99.93 | 0.17022 | 0.16822 | 0.20709 | RANDOM | 34.155 |
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] | |
-1.39 | -1.39 | 2.78 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.021 |
r_dihedral_angle_4_deg | 18.641 |
r_dihedral_angle_3_deg | 12.892 |
r_dihedral_angle_1_deg | 6.56 |
r_long_range_B_refined | 4.973 |
r_long_range_B_other | 4.973 |
r_scangle_other | 3.922 |
r_mcangle_it | 2.661 |
r_mcangle_other | 2.661 |
r_scbond_it | 2.661 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6134 |
Nucleic Acid Atoms | |
Solvent Atoms | 355 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XDS | data scaling |
Aimless | data scaling |
SHELXCD | phasing |
SHELXE | model building |
ARP/wARP | model building |
BUCCANEER | model building |
Coot | model building |
REFMAC | refinement |