7DKB
Stenotrophomonas maltophilia DPP7 in complex with Val-Tyr
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | 0.2M Amm Acetate, 20%w/v PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.49 | α = 90 |
b = 73.33 | β = 95.16 |
c = 151.82 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 95 | CCD | RAYONIX MX300HE | 2015-10-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9 | SPring-8 | BL44XU |
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 | 1.94 | 45.75 | 93.7 | 0.256 | 0.275 | 0.1 | 0.397 | 7.9 | 7.6 | 100498 | 18.556 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.94 | 1.97 | 60.1 | 1.487 | 0.576 | 0.397 | 1.4 | 7.5 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3WOL | 2.03 | 40 | 91951 | 4522 | 97.619 | 0.203 | 0.2009 | 0.2454 | 29.45 |
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] | |
0.867 | 0.443 | 0.819 | -1.738 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.28 |
r_dihedral_angle_4_deg | 17.156 |
r_dihedral_angle_3_deg | 16.906 |
r_dihedral_angle_1_deg | 6.904 |
r_lrange_it | 5.801 |
r_lrange_other | 5.783 |
r_scangle_it | 4.485 |
r_scangle_other | 4.485 |
r_mcangle_it | 3.215 |
r_mcangle_other | 3.215 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10658 |
Nucleic Acid Atoms | |
Solvent Atoms | 461 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
XDS | data scaling |
PHASER | phasing |