8Q3J
Crystal structure of mIL-38 in complex with a neutralizing Fab e04 fragment
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 281 | 27.5% (w/v) PEG 1500 100 mM SPG buffer, pH 8.7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 50.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.8 | α = 90 |
b = 66.94 | β = 104.727 |
c = 129.05 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER2 S 16M | 2019-09-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.9763 | PETRA III, EMBL c/o DESY | P14 (MX2) |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.35 | 70.11 | 99 | 0.99 | 16.41 | 6.4 | 50677 | 55.59 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.35 | 2.49 | 99.2 | 0.99 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.5 | 70.11 | 1.37 | 42084 | 4207 | 99.07 | 0.2328 | 0.2272 | 0.2826 | 62.28 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.7026 |
f_angle_d | 1.1084 |
f_chiral_restr | 0.0554 |
f_plane_restr | 0.0102 |
f_bond_d | 0.0087 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8793 |
Nucleic Acid Atoms | |
Solvent Atoms | 109 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
PHENIX | refinement |
MxCuBE | data collection |
MxCuBE | data collection |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | phasing |
Coot | model building |