5WDL
A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.27 M K/Na Tartrate, 22% PEG3350, 1 mM ZnCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.19 | 61.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.841 | α = 90 |
b = 140.299 | β = 90 |
c = 221.087 | 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 | Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 | 2017-04-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.97946 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rpim I (All) | 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 | 2.65 | 50 | 99.6 | 0.15 | 0.161 | 0.071 | 12.7 | 5.9 | 96577 | 34.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.65 | 2.7 | 98.5 | 1.721 | 1.068 | 0.498 | 0.564 | 1.7 | 5.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3PW3 | 2.625 | 49.105 | 1.33 | 96495 | 4868 | 98.5 | 0.1729 | 0.1708 | 0.2124 | 39.3289 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 9.471 |
f_angle_d | 0.479 |
f_chiral_restr | 0.039 |
f_plane_restr | 0.003 |
f_bond_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17387 |
Nucleic Acid Atoms | |
Solvent Atoms | 780 |
Heterogen Atoms | 108 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |