7OS5
Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (orthorhombic form OP)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 292 | 25% PEG3350, 0.2 M Li2SO4, 0.01% (w/v) heptane-1,2,3-triol, 0.1 M Tris pH 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.231 | α = 90 |
b = 91.142 | β = 90 |
c = 106.017 | γ = 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 PILATUS 6M | 2019-04-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9762 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.29 | 69.11 | 95.4 | 0.17 | 0.179 | 0.05 | 0.996 | 10.4 | 12.7 | 131038 | 19.77 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.29 | 1.4 | 64.7 | 2.008 | 2.113 | 0.639 | 0.4 | 1.5 | 10.4 |
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 (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7OS3 | 1.293 | 69.11 | 129695 | 1000 | 68.626 | 0.155 | 0.1547 | 0.1943 | RANDOM | 13.957 |
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] | |
0.99 | 0.012 | -1.002 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.227 |
r_dihedral_angle_4_deg | 18.097 |
r_dihedral_angle_3_deg | 12.404 |
r_rigid_bond_restr | 6.399 |
r_dihedral_angle_1_deg | 6.237 |
r_lrange_it | 4.522 |
r_lrange_other | 4.345 |
r_scangle_it | 3.869 |
r_scangle_other | 3.748 |
r_scbond_it | 3.26 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5303 |
Nucleic Acid Atoms | |
Solvent Atoms | 628 |
Heterogen Atoms | 61 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |