5OT0
The thermostable L-asparaginase from Thermococcus kodakarensis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1WLS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.8 | 294 | 0.09 M NPS, 0.1 M buffer system 2, pH 6.5-7.0, 28.5% (v/v) EDO_P8K from the Morpheus kit |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.74 | α = 72.13 |
b = 70.96 | β = 76.22 |
c = 107.73 | γ = 87.83 |
Symmetry | |
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Space Group | P 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 | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2016-07-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.18 | 99.58 | 97.4 | 0.06 | 0.07 | 1 | 10.06 | 3.5 | 98478 | 50 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.18 | 2.26 | 97.2 | 1.2 | 1.4 | 0.75 | 0.59 | 1.3 | 3.6 |
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 | 1WLS | 2.18 | 68.65 | 93578 | 4896 | 97.5 | 0.19536 | 0.19379 | 0.22391 | RANDOM | 77.078 |
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] | |
-0.46 | 1.33 | 1.14 | 0.01 | -0.57 | 0.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.071 |
r_dihedral_angle_4_deg | 19.013 |
r_dihedral_angle_3_deg | 16.715 |
r_dihedral_angle_1_deg | 7.279 |
r_long_range_B_refined | 6.747 |
r_long_range_B_other | 6.747 |
r_scangle_other | 4.342 |
r_mcangle_it | 3.885 |
r_mcangle_other | 3.885 |
r_scbond_it | 2.773 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15042 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHASER | phasing |
Coot | model building |
xia2 | data reduction |
Aimless | data scaling |