2VRK
Structure of a seleno-methionyl derivative of wild type arabinofuranosidase from Thermobacillus xylanilyticus
X-RAY DIFFRACTION
Crystallization
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.76 | 67.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 158 | α = 90 |
b = 158 | β = 90 |
c = 380 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 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 | 120 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.2 | 39.47 | 99.8 | 0.13 | 5.1 | 10.7 | 188045 | 37.35 |
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 | 2.32 | 99.7 | 0.46 | 1.6 | 10.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | SAD | NONE | 2.2 | 39.5 | 141193 | 1415 | 99.8 | 0.166 | 0.165 | 0.186 | 31.98 |
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] | |
2.0642 | 2.0642 | -4.1284 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.245 |
f_angle_d | 1.102 |
f_chiral_restr | 0.084 |
f_bond_d | 0.008 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11790 |
Nucleic Acid Atoms | |
Solvent Atoms | 1187 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |
HKL2MAP | phasing |